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sstadick / perbase

Per-base per-nucleotide depth analysis
MIT License
115 stars 13 forks source link

read counter #37

Closed colindaven closed 3 years ago

colindaven commented 3 years ago

nice tool, thanks.

Are you planning to integrated a pure read counter (per reference) option, surely you have the functionality already ? The only-depth is very close.

I use samtools idxstats for this at present, but am looking for independent confirmation for edge cases, etc.

Thanks

sstadick commented 3 years ago

I haven't used indexstats before. It looks like it just shows the total number of reads that mapped to each reference?

I'm not currently planning on adding that to perbase, but that may change in the near future as I'm doing some updating.

What is the edge case you are running into? https://github.com/biod/sambamba would likely be the best place to implement the same functionality.

colindaven commented 3 years ago

Yes, just total reads per bacterial/viral/human/fungal chromosome

Sambamba does not implement idxstats and it's written in D, so I'll pass. I'll supply a GTF/GFF to a tool like htseq-count or featureCounts for this then instead. However, that means a couple of extra dependencies in my metagenomic pipeline, which is not great. At least I can use internally for testing.

Thanks