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HCGB-IGTP / XICRA

Small RNAseq pipeline for paired-end reads
MIT License
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Biotype and featureCounts argument #38

Closed jonahcullen closed 2 years ago

jonahcullen commented 2 years ago

Hello, thank you for putting together this fantastic pipeline, I have been having fun digging through it all. I am processing PE small RNA-seq data through prep, QC, and trimm.

I had one question regarding the biotype module and specifically with featureCounts. Why is the -p flag included? I can see in the featureCounts doc that is for counting fragments instead of reads and is only applicable for PE reads (SE reads always counted as reads). I noticed with this flag included, it returns 0% Successfully assigned alignments, compared to without at >80%.

Perhaps I am misunderstanding the impact or purpose rather?

Thanks for your time, Jonah.

JFsanchezherrero commented 2 years ago

Hi there Jonah, I am glad to hear you find interesting and useful this pipeline.

I can see you opened another issue, I will be answering there later too.

Regarding the question you mentioned here about the biotype and featurecount flag I set -p as I understood is required for counting BAM files mapped using paired-end. It is true that it might not be required and if it produces these differences in statistics that you mentioned it definitely makes no sense to keep it.

I will further test and read about it and change it or maybe set it as optional in future versions of XICRA.

Thanks for your time too Best regards,

jonahcullen commented 2 years ago

Thank you for your prompt response!