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We are analyzing https://github.com/marcelm/cutadapt/issues/744.

Title:
How to handle reads with alternative adapters or primer sequences ยท Issue #744 ยท marcelm/cutadapt
Description:
Hi, It's a powerful tools for data analysis. I have a question when trimming primers from paired-end reads of amplicon. The sequencing data (e.g. forward_reads) likes: AAATTTaaaaaaaaCCCGGG and ...
Website Age:
17 years and 8 months (reg. 2007-10-09).

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Github.com is built with WORDPRESS.

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๐Ÿš€๐ŸŒ  Tremendous Traffic: 10M - 20M visitors per month


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Keywords {๐Ÿ”}

reads, revcomp, pairedend, marcelm, issue, fxfish, sign, data, commented, implement, search, cutadapt, aaattt, cccggg, rfq, swapped, version, navigation, pull, requests, actions, security, handle, alternative, adapters, primer, sequences, closed, likes, output, steps, owner, work, results, swapping, author, bbce, update, react, github, labels, projects, milestone, footer, skip, content, menu, product, solutions, resources,

Topics {โœ’๏ธ}

b4bc46e marcelm closed normal adapter search means recognizing โ€˜gggccc reversing complementary sequence comment metadata assignees paired-end reads single-end reads paired-end data combining 1st r1 swapped version resulted output data likes search cutadapt cutadapt 4 handle reads data analysis sequencing data swapped version unswapped version alternative adapters powerful tools trimming primers step commond functionality doesn implementing --revcomp makes sense function --revcomp assigned labels labels projects projects milestone milestone relationships personal information github 2st r2 ^cccggg --revcomp swapping r1 implement likes revcomp swapped output r1 swapping ^cccggg ^cccggg r2 skip jump sign question

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  • Already have an account?
  • Can I just use one step commond?
  • Can you say whether that would give you the result you want?

Schema {๐Ÿ—บ๏ธ}

DiscussionForumPosting:
      context:https://schema.org
      headline:How to handle reads with alternative adapters or primer sequences
      articleBody:Hi, It's a powerful tools for data analysis. I have a question when trimming primers from paired-end reads of amplicon. The sequencing data (e.g. forward_reads) likes: AAATTTaaaaaaaaCCCGGG and GGGCCCtttttttttTTTAAA (mixed), I want all output data likes: aaaaaaaa, which means recognizing โ€˜GGGCCC...TTTAAAโ€™ and reversing complementary sequence. I must do three steps to achive this, one using -g ^AAATTT -G ^CCCGGG, and another using -g ^CCCGGG -G ^AAATTT, at last combining 1st R1.fq and 2st R2.fq into the last R1.fq. Can I just use one step commond? -g -g or -g XXX|XXX Thanks. <!-- When reporting an issue, please include this information: - Cutadapt and Python version - How you installed the tool (conda or pip, for example) - Which command-line parameters you used If you report unexpected trimming behavior, this would also be helpful: - An example input read (or read pair) - The output that cutadapt produces - The output that you would have expected Feel free to delete this text before submitting your issue. -->
      author:
         url:https://github.com/fxfish
         type:Person
         name:fxfish
      datePublished:2023-11-30T09:32:07.000Z
      interactionStatistic:
         type:InteractionCounter
         interactionType:https://schema.org/CommentAction
         userInteractionCount:4
      url:https://github.com/744/cutadapt/issues/744
      context:https://schema.org
      headline:How to handle reads with alternative adapters or primer sequences
      articleBody:Hi, It's a powerful tools for data analysis. I have a question when trimming primers from paired-end reads of amplicon. The sequencing data (e.g. forward_reads) likes: AAATTTaaaaaaaaCCCGGG and GGGCCCtttttttttTTTAAA (mixed), I want all output data likes: aaaaaaaa, which means recognizing โ€˜GGGCCC...TTTAAAโ€™ and reversing complementary sequence. I must do three steps to achive this, one using -g ^AAATTT -G ^CCCGGG, and another using -g ^CCCGGG -G ^AAATTT, at last combining 1st R1.fq and 2st R2.fq into the last R1.fq. Can I just use one step commond? -g -g or -g XXX|XXX Thanks. <!-- When reporting an issue, please include this information: - Cutadapt and Python version - How you installed the tool (conda or pip, for example) - Which command-line parameters you used If you report unexpected trimming behavior, this would also be helpful: - An example input read (or read pair) - The output that cutadapt produces - The output that you would have expected Feel free to delete this text before submitting your issue. -->
      author:
         url:https://github.com/fxfish
         type:Person
         name:fxfish
      datePublished:2023-11-30T09:32:07.000Z
      interactionStatistic:
         type:InteractionCounter
         interactionType:https://schema.org/CommentAction
         userInteractionCount:4
      url:https://github.com/744/cutadapt/issues/744
Person:
      url:https://github.com/fxfish
      name:fxfish
      url:https://github.com/fxfish
      name:fxfish
InteractionCounter:
      interactionType:https://schema.org/CommentAction
      userInteractionCount:4
      interactionType:https://schema.org/CommentAction
      userInteractionCount:4

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