Question: Does two reads with opposite strand with same mapping location regarded as duplicates? #67

Open
Open
Question: Does two reads with opposite strand with same mapping location regarded as duplicates?#67

Description

@zztin
zztin
opened on Jul 5, 2023

Hi Andrew,

I have a nanopore sequencing library where one molecule could result in reads on both forward or reverse strands. I would like to know if preseq regard these pairs as "distinct" observation, or as "repeated" observation?

The definition of "distinct" observation is not very clearly stated in the documentation. I was trying to find it in the implementation:

Related lines:

preseq/src/load_data_for_complexity.cpp

Line 90 in c0fc953

curr_gr.get_start() != prev_gr.get_start())

Related class: GenomicRegion.hpp

It seems like get_start() is getting the smaller coordinate of a bam read?
If so, does it mean that both reverse and forward-mapped reads would be seen as the same molecule (same 'start') -- This is the desired behavior in my use case.

I would love to hear from you!

The command I used:

./preseq lc_extrap -B -o ./yield-estimates.txt <input-sorted-bam>

Software version:
v2.0 downloaded precompiled binary

Best,
Li-Ting

Activity

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Metadata

Metadata

Assignees

No one assigned

    Labels

    No labels
    No labels

    Type

    No type

    Projects

    No projects

      Milestone

      No milestone

      Relationships

      None yet

      Development

      No branches or pull requests

      Issue actions

      , 'i'); if (__m === '*' || __re.test(location.href)) { injectUserscript("// Add copy buttons to all 
       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 content
      Question: Does two reads with opposite strand with same mapping location regarded as duplicates? #67
      Open
      Open
      Question: Does two reads with opposite strand with same mapping location regarded as duplicates?#67
      Description
      @zztin
      zztin
      opened on Jul 5, 2023
      Hi Andrew,
      I have a nanopore sequencing library where one molecule could result in reads on both forward or reverse strands. I would like to know if preseq regard these pairs as "distinct" observation, or as "repeated" observation?
      The definition of "distinct" observation is not very clearly stated in the documentation. I was trying to find it in the implementation:
      Related lines:
      preseq/src/load_data_for_complexity.cpp
      
Line 90
in
c0fc953
       curr_gr.get_start() != prev_gr.get_start()) 

      
Related class: GenomicRegion.hpp
      It seems like get_start() is getting the smaller coordinate of a bam read?
      
If so, does it mean that both reverse and forward-mapped reads would be seen as the same molecule (same 'start') -- This is the desired behavior in my use case.
      I would love to hear from you!
      The command I used:
      ./preseq lc_extrap -B -o ./yield-estimates.txt <input-sorted-bam>

      Software version:
      
v2.0 downloaded precompiled binary
      Best,
      
Li-Ting
      Activity
      Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
      Metadata
      Metadata
      Assignees
      No one assigned
        Labels
        No labels
        No labels
        Type
        No type
        Projects
        No projects
          Milestone
          No milestone
          Relationships
          None yet
          Development
          No branches or pull requests
          Issue actions
          
, '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 content
          Question: Does two reads with opposite strand with same mapping location regarded as duplicates? #67
          Open
          Open
          Question: Does two reads with opposite strand with same mapping location regarded as duplicates?#67
          Description
          @zztin
          zztin
          opened on Jul 5, 2023
          Hi Andrew,
          I have a nanopore sequencing library where one molecule could result in reads on both forward or reverse strands. I would like to know if preseq regard these pairs as "distinct" observation, or as "repeated" observation?
          The definition of "distinct" observation is not very clearly stated in the documentation. I was trying to find it in the implementation:
          Related lines:
          preseq/src/load_data_for_complexity.cpp
          
Line 90
in
c0fc953
           curr_gr.get_start() != prev_gr.get_start()) 

          
Related class: GenomicRegion.hpp
          It seems like get_start() is getting the smaller coordinate of a bam read?
          
If so, does it mean that both reverse and forward-mapped reads would be seen as the same molecule (same 'start') -- This is the desired behavior in my use case.
          I would love to hear from you!
          The command I used:
          ./preseq lc_extrap -B -o ./yield-estimates.txt <input-sorted-bam>

          Software version:
          
v2.0 downloaded precompiled binary
          Best,
          
Li-Ting
          Activity
          Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
          Metadata
          Metadata
          Assignees
          No one assigned
            Labels
            No labels
            No labels
            Type
            No type
            Projects
            No projects
              Milestone
              No milestone
              Relationships
              None yet
              Development
              No branches or pull requests
              Issue actions
              
, '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 content
              Question: Does two reads with opposite strand with same mapping location regarded as duplicates? #67
              Open
              Open
              Question: Does two reads with opposite strand with same mapping location regarded as duplicates?#67
              Description
              @zztin
              zztin
              opened on Jul 5, 2023
              Hi Andrew,
              I have a nanopore sequencing library where one molecule could result in reads on both forward or reverse strands. I would like to know if preseq regard these pairs as "distinct" observation, or as "repeated" observation?
              The definition of "distinct" observation is not very clearly stated in the documentation. I was trying to find it in the implementation:
              Related lines:
              preseq/src/load_data_for_complexity.cpp
              
Line 90
in
c0fc953
               curr_gr.get_start() != prev_gr.get_start()) 

              
Related class: GenomicRegion.hpp
              It seems like get_start() is getting the smaller coordinate of a bam read?
              
If so, does it mean that both reverse and forward-mapped reads would be seen as the same molecule (same 'start') -- This is the desired behavior in my use case.
              I would love to hear from you!
              The command I used:
              ./preseq lc_extrap -B -o ./yield-estimates.txt <input-sorted-bam>

              Software version:
              
v2.0 downloaded precompiled binary
              Best,
              
Li-Ting
              Activity
              Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
              Metadata
              Metadata
              Assignees
              No one assigned
                Labels
                No labels
                No labels
                Type
                No type
                Projects
                No projects
                  Milestone
                  No milestone
                  Relationships
                  None yet
                  Development
                  No branches or pull requests
                  Issue actions
                  
, '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 content
                  Question: Does two reads with opposite strand with same mapping location regarded as duplicates? #67
                  Open
                  Open
                  Question: Does two reads with opposite strand with same mapping location regarded as duplicates?#67
                  Description
                  @zztin
                  zztin
                  opened on Jul 5, 2023
                  Hi Andrew,
                  I have a nanopore sequencing library where one molecule could result in reads on both forward or reverse strands. I would like to know if preseq regard these pairs as "distinct" observation, or as "repeated" observation?
                  The definition of "distinct" observation is not very clearly stated in the documentation. I was trying to find it in the implementation:
                  Related lines:
                  preseq/src/load_data_for_complexity.cpp
                  
Line 90
in
c0fc953
                   curr_gr.get_start() != prev_gr.get_start()) 

                  
Related class: GenomicRegion.hpp
                  It seems like get_start() is getting the smaller coordinate of a bam read?
                  
If so, does it mean that both reverse and forward-mapped reads would be seen as the same molecule (same 'start') -- This is the desired behavior in my use case.
                  I would love to hear from you!
                  The command I used:
                  ./preseq lc_extrap -B -o ./yield-estimates.txt <input-sorted-bam>

                  Software version:
                  
v2.0 downloaded precompiled binary
                  Best,
                  
Li-Ting
                  Activity
                  Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
                  Metadata
                  Metadata
                  Assignees
                  No one assigned
                    Labels
                    No labels
                    No labels
                    Type
                    No type
                    Projects
                    No projects
                      Milestone
                      No milestone
                      Relationships
                      None yet
                      Development
                      No branches or pull requests
                      Issue actions
                      
, '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 content
                      Question: Does two reads with opposite strand with same mapping location regarded as duplicates? #67
                      Open
                      Open
                      Question: Does two reads with opposite strand with same mapping location regarded as duplicates?#67
                      Description
                      @zztin
                      zztin
                      opened on Jul 5, 2023
                      Hi Andrew,
                      I have a nanopore sequencing library where one molecule could result in reads on both forward or reverse strands. I would like to know if preseq regard these pairs as "distinct" observation, or as "repeated" observation?
                      The definition of "distinct" observation is not very clearly stated in the documentation. I was trying to find it in the implementation:
                      Related lines:
                      preseq/src/load_data_for_complexity.cpp
                      
Line 90
in
c0fc953
                       curr_gr.get_start() != prev_gr.get_start()) 

                      
Related class: GenomicRegion.hpp
                      It seems like get_start() is getting the smaller coordinate of a bam read?
                      
If so, does it mean that both reverse and forward-mapped reads would be seen as the same molecule (same 'start') -- This is the desired behavior in my use case.
                      I would love to hear from you!
                      The command I used:
                      ./preseq lc_extrap -B -o ./yield-estimates.txt <input-sorted-bam>

                      Software version:
                      
v2.0 downloaded precompiled binary
                      Best,
                      
Li-Ting
                      Activity
                      Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
                      Metadata
                      Metadata
                      Assignees
                      No one assigned
                        Labels
                        No labels
                        No labels
                        Type
                        No type
                        Projects
                        No projects
                          Milestone
                          No milestone
                          Relationships
                          None yet
                          Development
                          No branches or pull requests
                          Issue actions
                          
, '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 content
                          Question: Does two reads with opposite strand with same mapping location regarded as duplicates? #67
                          Open
                          Open
                          Question: Does two reads with opposite strand with same mapping location regarded as duplicates?#67
                          Description
                          @zztin
                          zztin
                          opened on Jul 5, 2023
                          Hi Andrew,
                          I have a nanopore sequencing library where one molecule could result in reads on both forward or reverse strands. I would like to know if preseq regard these pairs as "distinct" observation, or as "repeated" observation?
                          The definition of "distinct" observation is not very clearly stated in the documentation. I was trying to find it in the implementation:
                          Related lines:
                          preseq/src/load_data_for_complexity.cpp
                          
Line 90
in
c0fc953
                           curr_gr.get_start() != prev_gr.get_start()) 

                          
Related class: GenomicRegion.hpp
                          It seems like get_start() is getting the smaller coordinate of a bam read?
                          
If so, does it mean that both reverse and forward-mapped reads would be seen as the same molecule (same 'start') -- This is the desired behavior in my use case.
                          I would love to hear from you!
                          The command I used:
                          ./preseq lc_extrap -B -o ./yield-estimates.txt <input-sorted-bam>

                          Software version:
                          
v2.0 downloaded precompiled binary
                          Best,
                          
Li-Ting
                          Activity
                          Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
                          Metadata
                          Metadata
                          Assignees
                          No one assigned
                            Labels
                            No labels
                            No labels
                            Type
                            No type
                            Projects
                            No projects
                              Milestone
                              No milestone
                              Relationships
                              None yet
                              Development
                              No branches or pull requests
                              Issue actions
                              
, '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 content
                              Question: Does two reads with opposite strand with same mapping location regarded as duplicates? #67
                              Open
                              Open
                              Question: Does two reads with opposite strand with same mapping location regarded as duplicates?#67
                              Description
                              @zztin
                              zztin
                              opened on Jul 5, 2023
                              Hi Andrew,
                              I have a nanopore sequencing library where one molecule could result in reads on both forward or reverse strands. I would like to know if preseq regard these pairs as "distinct" observation, or as "repeated" observation?
                              The definition of "distinct" observation is not very clearly stated in the documentation. I was trying to find it in the implementation:
                              Related lines:
                              preseq/src/load_data_for_complexity.cpp
                              
Line 90
in
c0fc953
                               curr_gr.get_start() != prev_gr.get_start()) 

                              
Related class: GenomicRegion.hpp
                              It seems like get_start() is getting the smaller coordinate of a bam read?
                              
If so, does it mean that both reverse and forward-mapped reads would be seen as the same molecule (same 'start') -- This is the desired behavior in my use case.
                              I would love to hear from you!
                              The command I used:
                              ./preseq lc_extrap -B -o ./yield-estimates.txt <input-sorted-bam>

                              Software version:
                              
v2.0 downloaded precompiled binary
                              Best,
                              
Li-Ting
                              Activity
                              Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
                              Metadata
                              Metadata
                              Assignees
                              No one assigned
                                Labels
                                No labels
                                No labels
                                Type
                                No type
                                Projects
                                No projects
                                  Milestone
                                  No milestone
                                  Relationships
                                  None yet
                                  Development
                                  No branches or pull requests
                                  Issue actions