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Bowtie2 local to global alignment for ancient DNA mode for BOWTIE2_ASSEMBLY_ALIGN #345

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merged 2 commits into from
Oct 19, 2022
Merged

Bowtie2 local to global alignment for ancient DNA mode for BOWTIE2_ASSEMBLY_ALIGN #345

merged 2 commits into from
Oct 19, 2022

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maxibor
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@maxibor maxibor commented Oct 18, 2022 •
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After some testing, I realized that the local alignemnt mode of bowtie2 in the ancient mode is posing problem as it soft-trim the ends of the reads, thus preventing the damage detection.
Going to global alignment mode solves this issue.

PR checklist

  • This comment contains a description of changes (with reason).
  • If you've fixed a bug or added code that should be tested, add tests!
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • CHANGELOG.md is updated.

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github-actions bot commented Oct 18, 2022 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 099a502

+| ✅ 156 tests passed       |+
#| ❔   1 tests were ignored |#
!| ❗   1 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your prefered methods description, e.g. add publication citation for this pipeline

❔ Tests ignored:

  • files_unchanged - File ignored due to lint config: lib/NfcoreTemplate.groovy

✅ Tests passed:

Run details

  • nf-core/tools version 2.6
  • Run at 2022-10-18 21:17:37

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maxibor commented Oct 18, 2022

With local alignment mode --very-sensitive-local (bad, soft-clipping removes damage on reads ends)
image

With global alignment mode --very-sensitive (good, the typical ancient DNA damage pattern is still observable)
image

@maxibor maxibor requested a review from jfy133 October 18, 2022 21:19
@maxibor maxibor requested a review from d4straub October 19, 2022 09:25
d4straub
d4straub approved these changes Oct 19, 2022
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LGTM

@jfy133 jfy133 merged commit 00cccfe into nf-core:dev Oct 19, 2022
@jfy133 jfy133 mentioned this pull request Feb 27, 2023
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@d4straub d4straub d4straub approved these changes

@jfy133 jfy133 jfy133 approved these changes

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@maxibor @jfy133 @d4straub