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Keywords {🔍}

aaa, readindel, cutadapt, barcode, adapter, readsnp, marcelm, score, error, gtcaaa, aatgtcaaa, adrianomartinelli, end, inputfastq, alignment, matrix, trimming, issue, start, files, commented, option, read, sign, sequence, readsnpend, output, trim, run, rename, tgtcaaa, edit, debug, unexpected, behavior, aaaaaaaaaa, infofileinfotsv, readsnpstart, infotsv, aaaaaaaaa, owner, anchored, indels, readnoerror, aatagtcaaa, tagtcaaa, errors, initialized, distances, scores,

Topics {✒️}

unexpected trimming behavior tsv output read-snp-start {barcode_1}{const_region_1}{barcode_2}{const_region_2}{barcode_3} expected read-snp-start fastq \ --info-file=info ~~~~~~~~~~ read-snp-end read-snp-end ~~~~~~~ read-indel-0--1 ~~~~ ~~~~~~ read-indel-1--1 ~~~~~~~ read-indel-2--1 ~~~~~~~~ read-indel-3--1 read-indel-2--1 read-indel-0--1 read-indel-1--1 read-indel-3--1 read-snp-0--1 ~~~~~~ read-snp-1--1 ~~~~~~ read-snp-2--1 read-snp-2--1 read-snp-1--1 comment metadata assignees taagtcaaa aaaaaaaaat read marcelm closed insights tsv read dynamic programming matrix info file read header ran cutadapt agains command-line parameters adapter trimming indel /dev/null input initialized incorrectly snp tsv file read fastq header info files quick fix fastq input anchored adapter option {adapter_name} 0 error rate issue aatgtcaaa aatgtcaaa initialized correctly f7bf154 sign

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Questions {❓}

• Already have an account?
• However, substitutions at the end are treated differently from substitutions at the start?
• It seems like indels at the start are not punished or counted as errors?

Schema {🗺️}

DiscussionForumPosting:
      context:https://schema.org
      headline:Unexpected trimming behavior
      articleBody:Hey! I am playing around with cutadapt to figure out if I can use it for our use case. I ran into the following issue: My target sequence is `AAAAAAAAAA` and I ran cutadapt agains the sequences shown below that are of the same length but with a substitution either at the start or the end of the sequence. I would have expected that with an overlap of 9 and 0 error rate both reads in the `input.fastq` are identified. However, substitutions at the end are treated differently from substitutions at the start? - Cutadapt and Python version: cutadapt 4.8 and Python 3.11.8 - How you installed the tool (conda or pip, for example): pip installed - Which command-line parameters you used: ```bash cutadapt -e 0 -O 9 \ -g AAAAAAAAAA \ -o /dev/null input.fastq \ --info-file=info.tsv ``` - My used `input.fastq` ```txt @read-snp-start TAAAAAAAAA + ~~~~~~~~~~ @read-snp-end- AAAAAAAAAT + ~~~~~~~~~~ ``` - The `info.tsv` output ```txt read-snp-start -1 TAAAAAAAAA ~~~~~~~~~~ read-snp-end- 0 0 9 AAAAAAAAA T 1 ~~~~~~~~~ ~ ``` - The output that you would have expected ```txt read-snp-start 0 1 10 T AAAAAAAAA 1 ~ ~~~~~~~~~ read-snp-end- 0 0 9 AAAAAAAAA T 1 ~~~~~~~~~ ~ ``` Maybe as a general background on what I try to achieve. I have reads structured like: `{barcode_1}{const_region_1}{barcode_2}{const_region_2}{barcode_3}` Each `barcode_N` can come from a set of ~100 different barcodes (i.e. the barcode a position `barcode_1` and `barcode_3` might be identical. My goal is to obtain a table indicating how often each barcode combinations was observed during the sequencing. My plan was to sequentially "trim" adapter sequences and using the `info.tsv` file to trace the barcode identifiers. Alternatively, I could maybe use the demultiplexing strategy, but this would lead to thousands of output files. Any suggestions of how to handle this and insights to the adapter trimming as described above are welcomed. Best, Adriano
      author:
         url:https://github.com/adrianomartinelli
         type:Person
         name:adrianomartinelli
      datePublished:2024-05-04T12:21:31.000Z
      interactionStatistic:
         type:InteractionCounter
         interactionType:https://schema.org/CommentAction
         userInteractionCount:5
      url:https://github.com/784/cutadapt/issues/784
      context:https://schema.org
      headline:Unexpected trimming behavior
      articleBody:Hey! I am playing around with cutadapt to figure out if I can use it for our use case. I ran into the following issue: My target sequence is `AAAAAAAAAA` and I ran cutadapt agains the sequences shown below that are of the same length but with a substitution either at the start or the end of the sequence. I would have expected that with an overlap of 9 and 0 error rate both reads in the `input.fastq` are identified. However, substitutions at the end are treated differently from substitutions at the start? - Cutadapt and Python version: cutadapt 4.8 and Python 3.11.8 - How you installed the tool (conda or pip, for example): pip installed - Which command-line parameters you used: ```bash cutadapt -e 0 -O 9 \ -g AAAAAAAAAA \ -o /dev/null input.fastq \ --info-file=info.tsv ``` - My used `input.fastq` ```txt @read-snp-start TAAAAAAAAA + ~~~~~~~~~~ @read-snp-end- AAAAAAAAAT + ~~~~~~~~~~ ``` - The `info.tsv` output ```txt read-snp-start -1 TAAAAAAAAA ~~~~~~~~~~ read-snp-end- 0 0 9 AAAAAAAAA T 1 ~~~~~~~~~ ~ ``` - The output that you would have expected ```txt read-snp-start 0 1 10 T AAAAAAAAA 1 ~ ~~~~~~~~~ read-snp-end- 0 0 9 AAAAAAAAA T 1 ~~~~~~~~~ ~ ``` Maybe as a general background on what I try to achieve. I have reads structured like: `{barcode_1}{const_region_1}{barcode_2}{const_region_2}{barcode_3}` Each `barcode_N` can come from a set of ~100 different barcodes (i.e. the barcode a position `barcode_1` and `barcode_3` might be identical. My goal is to obtain a table indicating how often each barcode combinations was observed during the sequencing. My plan was to sequentially "trim" adapter sequences and using the `info.tsv` file to trace the barcode identifiers. Alternatively, I could maybe use the demultiplexing strategy, but this would lead to thousands of output files. Any suggestions of how to handle this and insights to the adapter trimming as described above are welcomed. Best, Adriano
      author:
         url:https://github.com/adrianomartinelli
         type:Person
         name:adrianomartinelli
      datePublished:2024-05-04T12:21:31.000Z
      interactionStatistic:
         type:InteractionCounter
         interactionType:https://schema.org/CommentAction
         userInteractionCount:5
      url:https://github.com/784/cutadapt/issues/784
Person:
      url:https://github.com/adrianomartinelli
      name:adrianomartinelli
      url:https://github.com/adrianomartinelli
      name:adrianomartinelli
InteractionCounter:
      interactionType:https://schema.org/CommentAction
      userInteractionCount:5
      interactionType:https://schema.org/CommentAction
      userInteractionCount:5

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