hg38 reference

Download

https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/
https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.fa.gz

make index

$ gunzip hg38.fa.gz
$ samtools faidx hg38.fa
❯ ll
-rwxrwxrwx 1 ken ken 3.1G May 8 16:37 hg38.fa
-rwxrwxrwx 1 ken ken 19K May 8 16:38 hg38.fa.fai

Extract

extract chr21

samtools faidx hg38.fa chr21 > hg38.chr21.fa
samtools faidx hg38.chr21.fa

make chr21 index

$ samtools faidx hg38.chr21.fa
$ ll
-rwxrwxrwx 1 ken ken 46M May 8 16:39 hg38.chr21.fa
-rwxrwxrwx 1 ken ken 23 May 8 16:40 hg38.chr21.fa.fai
-rwxrwxrwx 1 ken ken 3.1G May 8 16:37 hg38.fa
-rwxrwxrwx 1 ken ken 19K May 8 16:38 hg38.fa.fai
$ samtools dict hg38.chr21.fa > hg38.chr21.dict

blocks\n(function() {\n function addCopyButtons() {\n document.querySelectorAll('pre code').forEach(function(codeBlock) {\n if (codeBlock.parentElement.hasAttribute('data-copy-added')) return;\n codeBlock.parentElement.setAttribute('data-copy-added', 'true');\n \n var btn = document.createElement('button');\n btn.textContent = 'Copy';\n btn.style.cssText = 'position:absolute;top:4px;right:4px;padding:2px 8px;font-size:11px;background:#4ecdc4;border:none;border-radius:4px;color:#1a1a2e;cursor:pointer;opacity:0.7;transition:opacity 0.2s;';\n btn.onmouseover = function() { this.style.opacity = '1'; };\n btn.onmouseout = function() { this.style.opacity = '0.7'; };\n btn.onclick = function() {\n navigator.clipboard.writeText(codeBlock.textContent).then(function() {\n btn.textContent = 'Copied!';\n setTimeout(function() { btn.textContent = 'Copy'; }, 1500);\n });\n };\n codeBlock.parentElement.style.position = 'relative';\n codeBlock.parentElement.appendChild(btn);\n });\n }\n \n addCopyButtons();\n \n // Re-run on dynamic content\n var observer = new MutationObserver(addCopyButtons);\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Add Copy Buttons to Code Blocks"); } } catch(__e) { console.warn('[Userscript:Add Copy Buttons to Code Blocks]', __e); } })(); (function(){ try { var __m = "github.com"; var __re = new RegExp('^' + "github\\.com" + ' Skip to contentNavigation Menu Sign inAppearance settings AI CODE CREATIONGitHub CopilotWrite better code with AI GitHub Copilot appDirect agents from issue to merge MCP RegistryIntegrate external tools DEVELOPER WORKFLOWSActionsAutomate any workflow CodespacesInstant dev environments IssuesPlan and track work Code ReviewManage code changes Code QualityEnforce quality at merge APPLICATION SECURITYGitHub Advanced SecurityFind and fix vulnerabilities Code securitySecure your code as you build Secret protectionStop leaks before they start EXPLOREWhy GitHub Documentation Blog Changelog Marketplace View all features BY COMPANY SIZEEnterprises Small and medium teams Startups Nonprofits BY USE CASEApp Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRYHealthcare Financial services Manufacturing Government View all industries View all solutions EXPLORE BY TOPICAI Software Development DevOps Security View all topics EXPLORE BY TYPECustomer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICESDocumentation Customer support Community forum Trust center Partners View all resources COMMUNITYGitHub SponsorsFund open source developers PROGRAMSSecurity Lab Maintainer Community GitHub Stars Archive Program REPOSITORIESTopics Trending Collections ENTERPRISE SOLUTIONSEnterprise platformAI-powered developer platform AVAILABLE ADD-ONSGitHub Advanced SecurityEnterprise-grade security features Copilot for BusinessEnterprise-grade AI features Premium SupportEnterprise-grade 24/7 support Pricing Sign in Sign upAppearance settings You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert KennethJHan /GenomeAnalysisTutorialPublic Notifications You must be signed in to change notification settings Fork 8 Star 20 Code Issues5 Pull requests0 Actions Projects Security and quality0 Insights Additional navigation options Code Issues Pull requests Actions Projects Security and quality Insights hg38 reference #2 Copy link Copy link Open Open hg38 reference#2 Copy link Assignees Description KennethJHan opened on May 8, 2021 Issue body actions hg38 reference Download https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/ https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.fa.gz make index $ gunzip hg38.fa.gz $ samtools faidx hg38.fa ❯ ll -rwxrwxrwx 1 ken ken 3.1G May 8 16:37 hg38.fa -rwxrwxrwx 1 ken ken 19K May 8 16:38 hg38.fa.fai Extract extract chr21 samtools faidx hg38.fa chr21 > hg38.chr21.fa samtools faidx hg38.chr21.fa make chr21 index $ samtools faidx hg38.chr21.fa $ ll -rwxrwxrwx 1 ken ken 46M May 8 16:39 hg38.chr21.fa -rwxrwxrwx 1 ken ken 23 May 8 16:40 hg38.chr21.fa.fai -rwxrwxrwx 1 ken ken 3.1G May 8 16:37 hg38.fa -rwxrwxrwx 1 ken ken 19K May 8 16:38 hg38.fa.fai $ samtools dict hg38.chr21.fa > hg38.chr21.dict Reactions are currently unavailable Activity Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment Metadata Metadata Assignees KennethJHan Labels No labelsNo labels Projects No projects Milestone No milestone Relationships None yet Development No branches or pull requests Issue actions Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact You can’t perform that action at this time. , 'i'); if (__m === '*' || __re.test(location.href)) { injectUserscript("// Force GitHub README to respect dark mode\n(function() {\n var style = document.createElement('style');\n style.textContent = '\n .markdown-body {\n color-scheme: dark light;\n }\n .markdown-body pre { background: #161b22 !important; }\n .markdown-body code { background: rgba(110, 118, 129, 0.4) !important; }\n .markdown-body table th, .markdown-body table td { border-color: #30363d !important; }\n .markdown-body img { background: #0d1117; }\n .markdown-body blockquote { border-left-color: #8b949e; }\n .markdown-body hr { border-color: #30363d; }\n ';\n document.head.appendChild(style);\n})();", "GitHub Dark Mode README Fix"); } } catch(__e) { console.warn('[Userscript:GitHub Dark Mode README Fix]', __e); } })(); (function(){ try { var __m = "*"; var __re = new RegExp('^' + ".*" + ' Skip to contentNavigation Menu Sign inAppearance settings AI CODE CREATIONGitHub CopilotWrite better code with AI GitHub Copilot appDirect agents from issue to merge MCP RegistryIntegrate external tools DEVELOPER WORKFLOWSActionsAutomate any workflow CodespacesInstant dev environments IssuesPlan and track work Code ReviewManage code changes Code QualityEnforce quality at merge APPLICATION SECURITYGitHub Advanced SecurityFind and fix vulnerabilities Code securitySecure your code as you build Secret protectionStop leaks before they start EXPLOREWhy GitHub Documentation Blog Changelog Marketplace View all features BY COMPANY SIZEEnterprises Small and medium teams Startups Nonprofits BY USE CASEApp Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRYHealthcare Financial services Manufacturing Government View all industries View all solutions EXPLORE BY TOPICAI Software Development DevOps Security View all topics EXPLORE BY TYPECustomer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICESDocumentation Customer support Community forum Trust center Partners View all resources COMMUNITYGitHub SponsorsFund open source developers PROGRAMSSecurity Lab Maintainer Community GitHub Stars Archive Program REPOSITORIESTopics Trending Collections ENTERPRISE SOLUTIONSEnterprise platformAI-powered developer platform AVAILABLE ADD-ONSGitHub Advanced SecurityEnterprise-grade security features Copilot for BusinessEnterprise-grade AI features Premium SupportEnterprise-grade 24/7 support Pricing Sign in Sign upAppearance settings You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert KennethJHan /GenomeAnalysisTutorialPublic Notifications You must be signed in to change notification settings Fork 8 Star 20 Code Issues5 Pull requests0 Actions Projects Security and quality0 Insights Additional navigation options Code Issues Pull requests Actions Projects Security and quality Insights hg38 reference #2 Copy link Copy link Open Open hg38 reference#2 Copy link Assignees Description KennethJHan opened on May 8, 2021 Issue body actions hg38 reference Download https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/ https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.fa.gz make index $ gunzip hg38.fa.gz $ samtools faidx hg38.fa ❯ ll -rwxrwxrwx 1 ken ken 3.1G May 8 16:37 hg38.fa -rwxrwxrwx 1 ken ken 19K May 8 16:38 hg38.fa.fai Extract extract chr21 samtools faidx hg38.fa chr21 > hg38.chr21.fa samtools faidx hg38.chr21.fa make chr21 index $ samtools faidx hg38.chr21.fa $ ll -rwxrwxrwx 1 ken ken 46M May 8 16:39 hg38.chr21.fa -rwxrwxrwx 1 ken ken 23 May 8 16:40 hg38.chr21.fa.fai -rwxrwxrwx 1 ken ken 3.1G May 8 16:37 hg38.fa -rwxrwxrwx 1 ken ken 19K May 8 16:38 hg38.fa.fai $ samtools dict hg38.chr21.fa > hg38.chr21.dict Reactions are currently unavailable Activity Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment Metadata Metadata Assignees KennethJHan Labels No labelsNo labels Projects No projects Milestone No milestone Relationships None yet Development No branches or pull requests Issue actions Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact You can’t perform that action at this time. , 'i'); if (__m === '*' || __re.test(location.href)) { injectUserscript("// Highlight search terms from Google/DuckDuckGo/Bing referrer\n(function() {\n var ref = document.referrer;\n var terms = [];\n \n if (ref.includes('google.com') || ref.includes('duckduckgo.com') || ref.includes('bing.com')) {\n var url = new URL(ref);\n var q = url.searchParams.get('q') || url.searchParams.get('p');\n if (q) {\n terms = q.split(/\\s+/).filter(function(t) { return t.length > 2; });\n }\n }\n \n if (terms.length === 0) return;\n \n var style = document.createElement('style');\n style.textContent = '.userscript-highlight { background: #fbbf24; color: #1a1a2e; padding: 1px 3px; border-radius: 2px; }';\n document.head.appendChild(style);\n \n function highlight(node) {\n if (node.nodeType === 3) { // text node\n var text = node.textContent;\n var found = false;\n terms.forEach(function(term) {\n var regex = new RegExp('(' + term.replace(/[.*+?^${}()|[\\]\\\\]/g, '\\\\') + ')', 'gi');\n if (regex.test(text)) {\n found = true;\n var frag = document.createDocumentFragment();\n var parts = text.split(regex);\n parts.forEach(function(part, i) {\n if (i % 2 === 0) {\n frag.appendChild(document.createTextNode(part));\n } else {\n var span = document.createElement('span');\n span.className = 'userscript-highlight';\n span.textContent = part;\n frag.appendChild(span);\n }\n });\n node.parentNode.replaceChild(frag, node);\n }\n });\n } else if (node.nodeType === 1 && node.childNodes) { // element\n var skipTags = ['SCRIPT', 'STYLE', 'NOSCRIPT', 'TEXTAREA', 'INPUT', 'SELECT'];\n if (!skipTags.includes(node.tagName)) {\n Array.from(node.childNodes).forEach(highlight);\n }\n }\n }\n \n highlight(document.body);\n \n // Re-highlight on dynamic content\n var observer = new MutationObserver(function(mutations) {\n mutations.forEach(function(m) {\n m.addedNodes.forEach(function(node) {\n if (node.nodeType === 1 || node.nodeType === 3) highlight(node);\n });\n });\n });\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Highlight Search Terms"); } } catch(__e) { console.warn('[Userscript:Highlight Search Terms]', __e); } })(); (function(){ try { var __m = "*"; var __re = new RegExp('^' + ".*" + ' Skip to contentNavigation Menu Sign inAppearance settings AI CODE CREATIONGitHub CopilotWrite better code with AI GitHub Copilot appDirect agents from issue to merge MCP RegistryIntegrate external tools DEVELOPER WORKFLOWSActionsAutomate any workflow CodespacesInstant dev environments IssuesPlan and track work Code ReviewManage code changes Code QualityEnforce quality at merge APPLICATION SECURITYGitHub Advanced SecurityFind and fix vulnerabilities Code securitySecure your code as you build Secret protectionStop leaks before they start EXPLOREWhy GitHub Documentation Blog Changelog Marketplace View all features BY COMPANY SIZEEnterprises Small and medium teams Startups Nonprofits BY USE CASEApp Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRYHealthcare Financial services Manufacturing Government View all industries View all solutions EXPLORE BY TOPICAI Software Development DevOps Security View all topics EXPLORE BY TYPECustomer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICESDocumentation Customer support Community forum Trust center Partners View all resources COMMUNITYGitHub SponsorsFund open source developers PROGRAMSSecurity Lab Maintainer Community GitHub Stars Archive Program REPOSITORIESTopics Trending Collections ENTERPRISE SOLUTIONSEnterprise platformAI-powered developer platform AVAILABLE ADD-ONSGitHub Advanced SecurityEnterprise-grade security features Copilot for BusinessEnterprise-grade AI features Premium SupportEnterprise-grade 24/7 support Pricing Sign in Sign upAppearance settings You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert KennethJHan /GenomeAnalysisTutorialPublic Notifications You must be signed in to change notification settings Fork 8 Star 20 Code Issues5 Pull requests0 Actions Projects Security and quality0 Insights Additional navigation options Code Issues Pull requests Actions Projects Security and quality Insights hg38 reference #2 Copy link Copy link Open Open hg38 reference#2 Copy link Assignees Description KennethJHan opened on May 8, 2021 Issue body actions hg38 reference Download https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/ https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.fa.gz make index $ gunzip hg38.fa.gz $ samtools faidx hg38.fa ❯ ll -rwxrwxrwx 1 ken ken 3.1G May 8 16:37 hg38.fa -rwxrwxrwx 1 ken ken 19K May 8 16:38 hg38.fa.fai Extract extract chr21 samtools faidx hg38.fa chr21 > hg38.chr21.fa samtools faidx hg38.chr21.fa make chr21 index $ samtools faidx hg38.chr21.fa $ ll -rwxrwxrwx 1 ken ken 46M May 8 16:39 hg38.chr21.fa -rwxrwxrwx 1 ken ken 23 May 8 16:40 hg38.chr21.fa.fai -rwxrwxrwx 1 ken ken 3.1G May 8 16:37 hg38.fa -rwxrwxrwx 1 ken ken 19K May 8 16:38 hg38.fa.fai $ samtools dict hg38.chr21.fa > hg38.chr21.dict Reactions are currently unavailable Activity Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment Metadata Metadata Assignees KennethJHan Labels No labelsNo labels Projects No projects Milestone No milestone Relationships None yet Development No branches or pull requests Issue actions Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact You can’t perform that action at this time. , 'i'); if (__m === '*' || __re.test(location.href)) { injectUserscript("// Strip utm_, fbclid, gclid, etc. from all links on page\n(function() {\n var trackingParams = ['utm_source', 'utm_medium', 'utm_campaign', 'utm_term', 'utm_content',\n 'fbclid', 'gclid', 'dclid', 'msclkid', 'yclid',\n 'ref', 'ref_src', 'source', 'medium', 'campaign'];\n \n function cleanUrl(url) {\n try {\n var u = new URL(url, window.location.origin);\n var changed = false;\n trackingParams.forEach(function(p) {\n if (u.searchParams.has(p)) {\n u.searchParams.delete(p);\n changed = true;\n }\n });\n return changed ? u.toString() : url;\n } catch (e) {\n return url;\n }\n }\n \n function cleanLinks() {\n document.querySelectorAll('a[href]').forEach(function(a) {\n var clean = cleanUrl(a.href);\n if (clean !== a.href) a.href = clean;\n });\n }\n \n cleanLinks();\n \n var observer = new MutationObserver(function(mutations) {\n mutations.forEach(function(m) {\n m.addedNodes.forEach(function(node) {\n if (node.nodeType === 1) {\n if (node.tagName === 'A') cleanLinks();\n node.querySelectorAll('a[href]').forEach(function(a) {\n var clean = cleanUrl(a.href);\n if (clean !== a.href) a.href = clean;\n });\n }\n });\n });\n });\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Remove Tracking Parameters from Links"); } } catch(__e) { console.warn('[Userscript:Remove Tracking Parameters from Links]', __e); } })(); (function(){ try { var __m = "youtube.com"; var __re = new RegExp('^' + "youtube\\.com" + ' Skip to contentNavigation Menu Sign inAppearance settings AI CODE CREATIONGitHub CopilotWrite better code with AI GitHub Copilot appDirect agents from issue to merge MCP RegistryIntegrate external tools DEVELOPER WORKFLOWSActionsAutomate any workflow CodespacesInstant dev environments IssuesPlan and track work Code ReviewManage code changes Code QualityEnforce quality at merge APPLICATION SECURITYGitHub Advanced SecurityFind and fix vulnerabilities Code securitySecure your code as you build Secret protectionStop leaks before they start EXPLOREWhy GitHub Documentation Blog Changelog Marketplace View all features BY COMPANY SIZEEnterprises Small and medium teams Startups Nonprofits BY USE CASEApp Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRYHealthcare Financial services Manufacturing Government View all industries View all solutions EXPLORE BY TOPICAI Software Development DevOps Security View all topics EXPLORE BY TYPECustomer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICESDocumentation Customer support Community forum Trust center Partners View all resources COMMUNITYGitHub SponsorsFund open source developers PROGRAMSSecurity Lab Maintainer Community GitHub Stars Archive Program REPOSITORIESTopics Trending Collections ENTERPRISE SOLUTIONSEnterprise platformAI-powered developer platform AVAILABLE ADD-ONSGitHub Advanced SecurityEnterprise-grade security features Copilot for BusinessEnterprise-grade AI features Premium SupportEnterprise-grade 24/7 support Pricing Sign in Sign upAppearance settings You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert KennethJHan /GenomeAnalysisTutorialPublic Notifications You must be signed in to change notification settings Fork 8 Star 20 Code Issues5 Pull requests0 Actions Projects Security and quality0 Insights Additional navigation options Code Issues Pull requests Actions Projects Security and quality Insights hg38 reference #2 Copy link Copy link Open Open hg38 reference#2 Copy link Assignees Description KennethJHan opened on May 8, 2021 Issue body actions hg38 reference Download https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/ https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.fa.gz make index $ gunzip hg38.fa.gz $ samtools faidx hg38.fa ❯ ll -rwxrwxrwx 1 ken ken 3.1G May 8 16:37 hg38.fa -rwxrwxrwx 1 ken ken 19K May 8 16:38 hg38.fa.fai Extract extract chr21 samtools faidx hg38.fa chr21 > hg38.chr21.fa samtools faidx hg38.chr21.fa make chr21 index $ samtools faidx hg38.chr21.fa $ ll -rwxrwxrwx 1 ken ken 46M May 8 16:39 hg38.chr21.fa -rwxrwxrwx 1 ken ken 23 May 8 16:40 hg38.chr21.fa.fai -rwxrwxrwx 1 ken ken 3.1G May 8 16:37 hg38.fa -rwxrwxrwx 1 ken ken 19K May 8 16:38 hg38.fa.fai $ samtools dict hg38.chr21.fa > hg38.chr21.dict Reactions are currently unavailable Activity Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment Metadata Metadata Assignees KennethJHan Labels No labelsNo labels Projects No projects Milestone No milestone Relationships None yet Development No branches or pull requests Issue actions Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact You can’t perform that action at this time. , 'i'); if (__m === '*' || __re.test(location.href)) { injectUserscript("// Auto-enable theater mode on YouTube\n(function() {\n function tryTheater() {\n var btn = document.querySelector('button[aria-label=\"Theater mode\"], ytd-player #player button[title=\"Theater mode\"]');\n if (btn && !btn.classList.contains('activated')) {\n btn.click();\n }\n }\n \n // Try immediately\n tryTheater();\n \n // Try after navigation (SPA)\n var lastUrl = location.href;\n setInterval(function() {\n if (location.href !== lastUrl) {\n lastUrl = location.href;\n setTimeout(tryTheater, 500);\n }\n }, 1000);\n \n // Also try on player load\n var observer = new MutationObserver(tryTheater);\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "YouTube Theater Mode Default"); } } catch(__e) { console.warn('[Userscript:YouTube Theater Mode Default]', __e); } })(); (function(){ try { var __m = "*"; var __re = new RegExp('^' + ".*" + ' Skip to contentNavigation Menu Sign inAppearance settings AI CODE CREATIONGitHub CopilotWrite better code with AI GitHub Copilot appDirect agents from issue to merge MCP RegistryIntegrate external tools DEVELOPER WORKFLOWSActionsAutomate any workflow CodespacesInstant dev environments IssuesPlan and track work Code ReviewManage code changes Code QualityEnforce quality at merge APPLICATION SECURITYGitHub Advanced SecurityFind and fix vulnerabilities Code securitySecure your code as you build Secret protectionStop leaks before they start EXPLOREWhy GitHub Documentation Blog Changelog Marketplace View all features BY COMPANY SIZEEnterprises Small and medium teams Startups Nonprofits BY USE CASEApp Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRYHealthcare Financial services Manufacturing Government View all industries View all solutions EXPLORE BY TOPICAI Software Development DevOps Security View all topics EXPLORE BY TYPECustomer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICESDocumentation Customer support Community forum Trust center Partners View all resources COMMUNITYGitHub SponsorsFund open source developers PROGRAMSSecurity Lab Maintainer Community GitHub Stars Archive Program REPOSITORIESTopics Trending Collections ENTERPRISE SOLUTIONSEnterprise platformAI-powered developer platform AVAILABLE ADD-ONSGitHub Advanced SecurityEnterprise-grade security features Copilot for BusinessEnterprise-grade AI features Premium SupportEnterprise-grade 24/7 support Pricing Sign in Sign upAppearance settings You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert KennethJHan /GenomeAnalysisTutorialPublic Notifications You must be signed in to change notification settings Fork 8 Star 20 Code Issues5 Pull requests0 Actions Projects Security and quality0 Insights Additional navigation options Code Issues Pull requests Actions Projects Security and quality Insights hg38 reference #2 Copy link Copy link Open Open hg38 reference#2 Copy link Assignees Description KennethJHan opened on May 8, 2021 Issue body actions hg38 reference Download https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/ https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.fa.gz make index $ gunzip hg38.fa.gz $ samtools faidx hg38.fa ❯ ll -rwxrwxrwx 1 ken ken 3.1G May 8 16:37 hg38.fa -rwxrwxrwx 1 ken ken 19K May 8 16:38 hg38.fa.fai Extract extract chr21 samtools faidx hg38.fa chr21 > hg38.chr21.fa samtools faidx hg38.chr21.fa make chr21 index $ samtools faidx hg38.chr21.fa $ ll -rwxrwxrwx 1 ken ken 46M May 8 16:39 hg38.chr21.fa -rwxrwxrwx 1 ken ken 23 May 8 16:40 hg38.chr21.fa.fai -rwxrwxrwx 1 ken ken 3.1G May 8 16:37 hg38.fa -rwxrwxrwx 1 ken ken 19K May 8 16:38 hg38.fa.fai $ samtools dict hg38.chr21.fa > hg38.chr21.dict Reactions are currently unavailable Activity Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment Metadata Metadata Assignees KennethJHan Labels No labelsNo labels Projects No projects Milestone No milestone Relationships None yet Development No branches or pull requests Issue actions Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact You can’t perform that action at this time. , 'i'); if (__m === '*' || __re.test(location.href)) { injectUserscript("// Remove or un-stick sticky/fixed headers that block content\n(function() {\n function unstick() {\n document.querySelectorAll('header, nav, [role=\"banner\"], .header, .navbar, .sticky, .fixed-top, [style*=\"position: fixed\"], [style*=\"position:sticky\"]').forEach(function(el) {\n if (el.style.position === 'fixed' || el.style.position === 'sticky' || \n getComputedStyle(el).position === 'fixed' || getComputedStyle(el).position === 'sticky') {\n el.style.position = 'static';\n el.style.top = 'auto';\n el.style.zIndex = 'auto';\n }\n });\n }\n \n unstick();\n \n var observer = new MutationObserver(unstick);\n observer.observe(document.body, { childList: true, subtree: true, attributes: true, attributeFilter: ['style', 'class'] });\n})();", "Kill Sticky Headers"); } } catch(__e) { console.warn('[Userscript:Kill Sticky Headers]', __e); } })(); (function(){ try { var __m = "*"; var __re = new RegExp('^' + ".*" + ' Skip to contentNavigation Menu Sign inAppearance settings AI CODE CREATIONGitHub CopilotWrite better code with AI GitHub Copilot appDirect agents from issue to merge MCP RegistryIntegrate external tools DEVELOPER WORKFLOWSActionsAutomate any workflow CodespacesInstant dev environments IssuesPlan and track work Code ReviewManage code changes Code QualityEnforce quality at merge APPLICATION SECURITYGitHub Advanced SecurityFind and fix vulnerabilities Code securitySecure your code as you build Secret protectionStop leaks before they start EXPLOREWhy GitHub Documentation Blog Changelog Marketplace View all features BY COMPANY SIZEEnterprises Small and medium teams Startups Nonprofits BY USE CASEApp Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRYHealthcare Financial services Manufacturing Government View all industries View all solutions EXPLORE BY TOPICAI Software Development DevOps Security View all topics EXPLORE BY TYPECustomer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICESDocumentation Customer support Community forum Trust center Partners View all resources COMMUNITYGitHub SponsorsFund open source developers PROGRAMSSecurity Lab Maintainer Community GitHub Stars Archive Program REPOSITORIESTopics Trending Collections ENTERPRISE SOLUTIONSEnterprise platformAI-powered developer platform AVAILABLE ADD-ONSGitHub Advanced SecurityEnterprise-grade security features Copilot for BusinessEnterprise-grade AI features Premium SupportEnterprise-grade 24/7 support Pricing Sign in Sign upAppearance settings You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert KennethJHan /GenomeAnalysisTutorialPublic Notifications You must be signed in to change notification settings Fork 8 Star 20 Code Issues5 Pull requests0 Actions Projects Security and quality0 Insights Additional navigation options Code Issues Pull requests Actions Projects Security and quality Insights hg38 reference #2 Copy link Copy link Open Open hg38 reference#2 Copy link Assignees Description KennethJHan opened on May 8, 2021 Issue body actions hg38 reference Download https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/ https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.fa.gz make index $ gunzip hg38.fa.gz $ samtools faidx hg38.fa ❯ ll -rwxrwxrwx 1 ken ken 3.1G May 8 16:37 hg38.fa -rwxrwxrwx 1 ken ken 19K May 8 16:38 hg38.fa.fai Extract extract chr21 samtools faidx hg38.fa chr21 > hg38.chr21.fa samtools faidx hg38.chr21.fa make chr21 index $ samtools faidx hg38.chr21.fa $ ll -rwxrwxrwx 1 ken ken 46M May 8 16:39 hg38.chr21.fa -rwxrwxrwx 1 ken ken 23 May 8 16:40 hg38.chr21.fa.fai -rwxrwxrwx 1 ken ken 3.1G May 8 16:37 hg38.fa -rwxrwxrwx 1 ken ken 19K May 8 16:38 hg38.fa.fai $ samtools dict hg38.chr21.fa > hg38.chr21.dict Reactions are currently unavailable Activity Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment Metadata Metadata Assignees KennethJHan Labels No labelsNo labels Projects No projects Milestone No milestone Relationships None yet Development No branches or pull requests Issue actions Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact You can’t perform that action at this time. , 'i'); if (__m === '*' || __re.test(location.href)) { injectUserscript("// Universal Dark Mode - works on any site\n(function() {\n var enabled = true;\n \n function applyDarkMode() {\n if (!enabled) return;\n \n // Create style element if it doesn't exist\n var style = document.getElementById('universal-dark-mode-style');\n if (!style) {\n style = document.createElement('style');\n style.id = 'universal-dark-mode-style';\n document.head.appendChild(style);\n }\n \n // Dark mode CSS - inverts colors but preserves images/video\n style.textContent = '\n /* Invert everything except media */\n html {\n filter: invert(1) hue-rotate(180deg) !important;\n background: #1a1a2e !important;\n }\n \n /* Restore images, videos, iframes, canvas */\n img, video, iframe, canvas, svg, picture, [style*=\"background-image\"] {\n filter: invert(1) hue-rotate(180deg) !important;\n }\n \n /* Preserve specific elements that should not be inverted */\n .no-dark-mode, .no-dark-mode *,\n [data-theme=\"light\"], [data-theme=\"light\"],\n .ace_editor, .ace_editor *,\n .CodeMirror, .CodeMirror *,\n .monaco-editor, .monaco-editor *,\n .markdown-body pre, .markdown-body pre *,\n .highlight, .highlight *,\n pre code, pre code * {\n filter: none !important;\n }\n \n /* Fix common UI elements */\n .modal, .popup, .dropdown-menu, .tooltip, .popover {\n filter: invert(1) hue-rotate(180deg) !important;\n background: #2d2d44 !important;\n border-color: #444 !important;\n }\n \n /* Scrollbars */\n ::-webkit-scrollbar { background: #1a1a2e !important; }\n ::-webkit-scrollbar-thumb { background: #444 !important; }\n ::-webkit-scrollbar-thumb:hover { background: #555 !important; }\n \n /* Selection */\n ::selection { background: #4ecdc4 !important; color: #1a1a2e !important; }\n ::-moz-selection { background: #4ecdc4 !important; color: #1a1a2e !important; }\n ';\n }\n \n function removeDarkMode() {\n var style = document.getElementById('universal-dark-mode-style');\n if (style) style.remove();\n }\n \n // Toggle with Alt+Shift+D\n document.addEventListener('keydown', function(e) {\n if (e.altKey && e.shiftKey && e.key === 'D') {\n e.preventDefault();\n enabled = !enabled;\n if (enabled) {\n applyDarkMode();\n console.log('[Universal Dark Mode] Enabled');\n } else {\n removeDarkMode();\n console.log('[Universal Dark Mode] Disabled');\n }\n }\n });\n \n // Apply on load\n applyDarkMode();\n \n // Re-apply on dynamic content\n var observer = new MutationObserver(function(mutations) {\n if (enabled && !document.getElementById('universal-dark-mode-style')) {\n applyDarkMode();\n }\n });\n observer.observe(document.head, { childList: true });\n \n console.log('[Universal Dark Mode] Loaded - Press Alt+Shift+D to toggle');\n})();", "Universal Dark Mode"); } } catch(__e) { console.warn('[Userscript:Universal Dark Mode]', __e); } })(); })(); Skip to contentNavigation Menu Sign inAppearance settings AI CODE CREATIONGitHub CopilotWrite better code with AI GitHub Copilot appDirect agents from issue to merge MCP RegistryIntegrate external tools DEVELOPER WORKFLOWSActionsAutomate any workflow CodespacesInstant dev environments IssuesPlan and track work Code ReviewManage code changes Code QualityEnforce quality at merge APPLICATION SECURITYGitHub Advanced SecurityFind and fix vulnerabilities Code securitySecure your code as you build Secret protectionStop leaks before they start EXPLOREWhy GitHub Documentation Blog Changelog Marketplace View all features BY COMPANY SIZEEnterprises Small and medium teams Startups Nonprofits BY USE CASEApp Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRYHealthcare Financial services Manufacturing Government View all industries View all solutions EXPLORE BY TOPICAI Software Development DevOps Security View all topics EXPLORE BY TYPECustomer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICESDocumentation Customer support Community forum Trust center Partners View all resources COMMUNITYGitHub SponsorsFund open source developers PROGRAMSSecurity Lab Maintainer Community GitHub Stars Archive Program REPOSITORIESTopics Trending Collections ENTERPRISE SOLUTIONSEnterprise platformAI-powered developer platform AVAILABLE ADD-ONSGitHub Advanced SecurityEnterprise-grade security features Copilot for BusinessEnterprise-grade AI features Premium SupportEnterprise-grade 24/7 support Pricing Sign in Sign upAppearance settings You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert KennethJHan /GenomeAnalysisTutorialPublic Notifications You must be signed in to change notification settings Fork 8 Star 20 Code Issues5 Pull requests0 Actions Projects Security and quality0 Insights Additional navigation options Code Issues Pull requests Actions Projects Security and quality Insights hg38 reference #2 Copy link Copy link Open Open hg38 reference#2 Copy link Assignees Description KennethJHan opened on May 8, 2021 Issue body actions hg38 reference Download https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/ https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.fa.gz make index $ gunzip hg38.fa.gz $ samtools faidx hg38.fa ❯ ll -rwxrwxrwx 1 ken ken 3.1G May 8 16:37 hg38.fa -rwxrwxrwx 1 ken ken 19K May 8 16:38 hg38.fa.fai Extract extract chr21 samtools faidx hg38.fa chr21 > hg38.chr21.fa samtools faidx hg38.chr21.fa make chr21 index $ samtools faidx hg38.chr21.fa $ ll -rwxrwxrwx 1 ken ken 46M May 8 16:39 hg38.chr21.fa -rwxrwxrwx 1 ken ken 23 May 8 16:40 hg38.chr21.fa.fai -rwxrwxrwx 1 ken ken 3.1G May 8 16:37 hg38.fa -rwxrwxrwx 1 ken ken 19K May 8 16:38 hg38.fa.fai $ samtools dict hg38.chr21.fa > hg38.chr21.dict Reactions are currently unavailable Activity Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment Metadata Metadata Assignees KennethJHan Labels No labelsNo labels Projects No projects Milestone No milestone Relationships None yet Development No branches or pull requests Issue actions Footer © 2026 GitHub, Inc. Footer navigation Terms Privacy Security Status Community Docs Contact You can’t perform that action at this time.