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fix: simpler three prime QuantSeq cutadapt setup #78
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…p in the config.yaml for the 3' test
…ly-a` flag available
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I have a doubt regarding the cutadapt step that I mentioned in the corresponding section.
We have now tested this on some current QuantSeq data, and the results seem to add up, even though there aren't any specific
We in this instance get:
Even when accounting for the
As noted, these have to be basepairs removed by removing reads that are too short, plus possibly the |
🤖 I have created a release *beep* *boop* --- ## [2.5.2](v2.5.1...v2.5.2) (2023-09-14) ### Bug Fixes * simpler three prime QuantSeq cutadapt setup ([#78](#78)) ([ecc9ab7](ecc9ab7)) * update samtools.yaml to latest `1.17` and update github actions ([#75](#75)) ([0fe7948](0fe7948)) ### Performance Improvements * bump datavzrd wrapper to 2.6.0 and general bug fixes ([#80](#80)) ([657c465](657c465)) --- This PR was generated with [Release Please](https://github.com/googleapis/release-please). See [documentation](https://github.com/googleapis/release-please#release-please). Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
I have tested this on actual QuantSeq data, and the cutadapt setup in this PR yields mostly the same results that the complicated previous three step setup recommended by Lexogen gave. It seems to be a bit more aggressive in the poly-A tail removal, but this should not affect results much. And it greatly simplifies the workflow setup.