Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

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

Open
4 tasks done
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

Comments

@li1311139481
Copy link

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?

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

1 participant