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Add post-trimming fragment length check / reporting #25

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pinin4fjords opened this issue Feb 20, 2024 · 1 comment
Open

Add post-trimming fragment length check / reporting #25

pinin4fjords opened this issue Feb 20, 2024 · 1 comment
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enhancement New feature or request
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@pinin4fjords
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Description of feature

Not sure of tool for this- Ribo-seQC? That will require some CLI engineering or templating on the nf-core modules though

@pinin4fjords pinin4fjords added the enhancement New feature or request label Feb 20, 2024
@pinin4fjords pinin4fjords added this to the v1.10 milestone Feb 20, 2024
@pinin4fjords pinin4fjords changed the title Add fragment length check Add post-trimming fragment length check / reporting Feb 20, 2024
@FelixKrueger
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The fragment lengths of the input files are already reported via a FastQC report on the trimmed FastQ files (already part of the MultiQC report. This might, however, be somewhat different to reporting the the same stats only for aligned reads.

We (i.e. @iraiosub) are currently looking at Ribo-seQC (which seems to produce rich and in-depth reports) as a potential additional module for the Ribo-seq workflow.

Most of the QC steps currently (Ribo-tish, Ribotricer, or potentially Ribo-seQC) seem to be sample specific, so it might be advisable to write a MultiQC tool that supports the conversion of tool-specific QC tables into a nice multi-sample QC plot in MultiQC.

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