use featureCounts or htseq-count instead of samtools idxstats for counting ?

MHH-RCUG / Wochenende

Deprecated see https://github.com/MHH-RCUG/nf_wochenende : A whole Genome/Metagenome Sequencing Alignment Pipeline in Python3

https://github.com/MHH-RCUG/nf_wochenende

MIT License

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Closed colindaven closed 3 years ago

colindaven commented 3 years ago

optional
which is easier in usage and output ?
add to conda env
especially for PE read counts, see 2x38bp vs 1x76bp alignment and count analysis issue on gitlab

colindaven commented 3 years ago

Not really plug in replacements without converting ref fa or fa.fai to BED / GFF3 / GTF format or similar