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sdparekh / zUMIs

zUMIs: A fast and flexible pipeline to process RNA sequencing data with UMIs
GNU General Public License v3.0
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Read count table for intergenic, ambiguous, unmapped reads #293

Closed pm-Genome2021 closed 2 years ago

pm-Genome2021 commented 2 years ago

Is your feature request related to a problem? Please describe. We need to compare genomic distribution of reads from a non-UMI based method with a UMI-based method. While there are count tables for exonic, intronic reads and intron-exon reads, I couldn't find counts for intergenic and even unambiguous and unmapped reads from the plot in the features pdf file. I can generate this outside of zUMIs but it would be nice to have a table generated within this pipeline. Please let me know if it is already available somewhere and I have missed it.

Describe the solution you'd like Count table containing the number of reads for each category displayed in the bar plot in features pdf file.

Describe alternatives you've considered Running QC tools outside of zUMIs on read mapping.

Additional context Add any other context or screenshots about the feature request here.

cziegenhain commented 2 years ago

These are found under zUMIs_output/stats/*.readspercell.txt.

pm-Genome2021 commented 2 years ago

That's awesome. Thank you for your quick reply & for all your work on this pipeline!