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Keywords {🔍}

chrr, read, slash, mates, names, issue, sign, bislheacbfgacxx, projects, commented, collaborator, fix, committed, added, navigation, pull, requests, actions, security, omitting, qname, truncating, closed, roningw, omit, characters, fastq, files, xcatagcga, tagggttagggttagggttagggtt, ffaddfhhcfhjjjcgdhijgg, taaccctaaccctaaccctaaccct, cccfffffhhhhhjjijiijjjjii, truncations, reads, change, enhancement, commit, ytzup, github, milestone, footer, skip, content, menu, product, solutions, resources, open, source,

Topics {✒️}

activity ronin-gw mentioned ch4rr0 edits collaborator fix committed paired-end fastq files omit slash mate slash mates projects milestone ch4rr0 closed match read names ch4rr0 fastq files reads read names issue illumina format additional strings sl-hea milestone relationships recent commit github completed sign end read bi commit sign skip jump printreadname truncated order whitespace heads encode c3bfgacxx omitted truncations pairs include change release assigned references address output provided 👍 react v2 free join

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DiscussionForumPosting:
      context:https://schema.org
      headline:Omitting slash mates (/1 or /2) in read names before QNAME truncating
      articleBody:In [`printReadName`](https://github.com/BenLangmead/bowtie2/blob/eff7f6e0265e805f5e10fd6dedf4266bdb5ce64d/sam.h#L216-L240), read names are truncated by following order: 1. Omit slash mate (`/1` or `/2`) from the end of a read name 2. Keep first 255 characters 3. Ignore characters after the first whitespace However, read names in some fastq files (maybe following the old illumina format) can have both slash mates and additional strings. For example, these are the heads of the paired-end fastq files I got from the [ENCODE](https://www.encodeproject.org/experiments/ENCSR975GZA/). ``` @BI:SL-HEA:C3BFGACXX:2:2316:10503:45861/1 1:X:0:CATAGCGA TAGGGTTAGGGTTAGGGTTAGGGTT + @@@FFADDFHHCFHJJJCGDHIJGG ``` ``` @BI:SL-HEA:C3BFGACXX:2:2316:10503:45861/2 1:X:0:CATAGCGA TAACCCTAACCCTAACCCTAACCCT + CCCFFFFFHHHHHJJIJIIJJJJII ``` So I think "slash mates" should be omitted *after* the other truncations to match read names as pairs.
      author:
         url:https://github.com/ronin-gw
         type:Person
         name:ronin-gw
      datePublished:2019-09-24T10:18:11.000Z
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      url:https://github.com/265/bowtie2/issues/265
      context:https://schema.org
      headline:Omitting slash mates (/1 or /2) in read names before QNAME truncating
      articleBody:In [`printReadName`](https://github.com/BenLangmead/bowtie2/blob/eff7f6e0265e805f5e10fd6dedf4266bdb5ce64d/sam.h#L216-L240), read names are truncated by following order: 1. Omit slash mate (`/1` or `/2`) from the end of a read name 2. Keep first 255 characters 3. Ignore characters after the first whitespace However, read names in some fastq files (maybe following the old illumina format) can have both slash mates and additional strings. For example, these are the heads of the paired-end fastq files I got from the [ENCODE](https://www.encodeproject.org/experiments/ENCSR975GZA/). ``` @BI:SL-HEA:C3BFGACXX:2:2316:10503:45861/1 1:X:0:CATAGCGA TAGGGTTAGGGTTAGGGTTAGGGTT + @@@FFADDFHHCFHJJJCGDHIJGG ``` ``` @BI:SL-HEA:C3BFGACXX:2:2316:10503:45861/2 1:X:0:CATAGCGA TAACCCTAACCCTAACCCTAACCCT + CCCFFFFFHHHHHJJIJIIJJJJII ``` So I think "slash mates" should be omitted *after* the other truncations to match read names as pairs.
      author:
         url:https://github.com/ronin-gw
         type:Person
         name:ronin-gw
      datePublished:2019-09-24T10:18:11.000Z
      interactionStatistic:
         type:InteractionCounter
         interactionType:https://schema.org/CommentAction
         userInteractionCount:3
      url:https://github.com/265/bowtie2/issues/265
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      url:https://github.com/ronin-gw
      name:ronin-gw
      url:https://github.com/ronin-gw
      name:ronin-gw
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      interactionType:https://schema.org/CommentAction
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      interactionType:https://schema.org/CommentAction
      userInteractionCount:3

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