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🚀🌠 Tremendous Traffic: 10M - 20M visitors per month


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Keywords {🔍}

marcelm, cutadapt, pairedend, length, sign, reads, issue, files, feature, shorten, separate, values, navigation, pull, requests, actions, security, request, closed, dear, working, work, lengths, trimming, adapter, rfastqgz, read, add, uppercase, option, variant, added, github, labels, projects, milestone, footer, skip, content, menu, product, solutions, resources, open, source, enterprise, pricing, search, jump, public,

Topics {✒️}

shorten paired-end reads paired-end support cutadapt --pair-filter comment metadata assignees paired-end trimming paired-end files feature dear community cutadapt didn properly paired trimmed reads cutadapt 40ea156 sign fantastic tool frequently work practically speaking length parameter minimum-length 20 15 --discard-untrimmed fixed length current approach separate rounds valid pairs redundant work makes sense lowercase variant update cli assigned labels labels projects projects milestone milestone relationships resulting files separate values actively working specific lengths uppercase variant github shortening r1 shorten reads gz r2 15 --length 20 trimming filter add option added files values working

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DiscussionForumPosting:
      context:https://schema.org
      headline:Feature request: shorten paired-end reads with separate values for --length
      articleBody:Dear developer, dear community, thank you for actively working on this fantastic tool! I frequently work with paired-end files that I need to shorten to specific lengths that are not equal for both reads. Practically speaking, I would like to apply the --length parameter with two different values during paired-end trimming. Something like the following, which is currently not working: ``` cutadapt --pair-filter any --minimum-length 20:15 --length 20:15 --discard-untrimmed -e 0.1 -g ADAPTER1 -G ADAPTER2 -o R1.out -p R2 out R1.fastq.gz R2.fastq.gz ``` The resulting files should contain trimmed reads that are shortened to a fixed length, in this case 20 and 15 bases for read 1 and read 2, respectively. My current approach is to ensure that both files are properly paired and then perform two separate rounds of trimming, one for each file. After that I further process both files to filter the valid pairs. This seems like a lot of redundant work that cutadapt is in principle able to do. Would be great to have this feature in cutadapt! Is this something that you can foresee to implement in the near future? Thanks!
      author:
         url:https://github.com/MaWeffm
         type:Person
         name:MaWeffm
      datePublished:2024-06-04T09:37:33.000Z
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      context:https://schema.org
      headline:Feature request: shorten paired-end reads with separate values for --length
      articleBody:Dear developer, dear community, thank you for actively working on this fantastic tool! I frequently work with paired-end files that I need to shorten to specific lengths that are not equal for both reads. Practically speaking, I would like to apply the --length parameter with two different values during paired-end trimming. Something like the following, which is currently not working: ``` cutadapt --pair-filter any --minimum-length 20:15 --length 20:15 --discard-untrimmed -e 0.1 -g ADAPTER1 -G ADAPTER2 -o R1.out -p R2 out R1.fastq.gz R2.fastq.gz ``` The resulting files should contain trimmed reads that are shortened to a fixed length, in this case 20 and 15 bases for read 1 and read 2, respectively. My current approach is to ensure that both files are properly paired and then perform two separate rounds of trimming, one for each file. After that I further process both files to filter the valid pairs. This seems like a lot of redundant work that cutadapt is in principle able to do. Would be great to have this feature in cutadapt! Is this something that you can foresee to implement in the near future? Thanks!
      author:
         url:https://github.com/MaWeffm
         type:Person
         name:MaWeffm
      datePublished:2024-06-04T09:37:33.000Z
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      url:https://github.com/788/cutadapt/issues/788
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      name:MaWeffm
      url:https://github.com/MaWeffm
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