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Does alignmentSieve not support single-ended sequencing data? #1317

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li1311139481 opened this issue Jul 4, 2024 · 0 comments
Open
4 tasks done

Does alignmentSieve not support single-ended sequencing data? #1317

li1311139481 opened this issue Jul 4, 2024 · 0 comments

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@li1311139481
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li1311139481 commented Jul 4, 2024

Welcome to deepTools GitHub repository! Before opening the issue please check
that the following requirements are met :

  • Search whether this issue (or a similar issue) has been solved before
    using the search tab above. Link the previous issue if appropriate below.
    https://www.biostars.org/p/9582427/#9598279
  • Paste your deepTools version (deeptools --version) and your python
    version (python --version) below.
    deeptools 3.5.5
    Python 3.10.12
  • Paste the full deepTools command that produces the issue below
    (ignore if you simply spotted the issue in the code/documentation).
    alignmentSieve -p ${THREADS} --shift 4 -5 --blackListFileName ${BLACKLIST} -b ${BOWTIE2}.clean.bam -o ${BOWTIE2}.shift.tmp
  • Paste the output printed on screen from the command that produces the issue
    below (ignore if you simply spotted the issue in the code/documentation).
    no error. but the ${BOWTIE2}.shift.tmp haven't reads infomation

my input data is single-end data. when i use
alignmentSieve -p ${THREADS} --ATACshift --blackListFileName ${BLACKLIST} -b ${BOWTIE2}.clean.bam -o ${BOWTIE2}.shift.tmp
i can get right result. Is it possible for alignmentSieve to support single-ended data?
If not, what should I do?

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