Obtaining coverage for rna-seq data
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18 months ago
rotemkat ▴ 10

I have many bam files (containing rna-seq data), and i need to obtain the total coverage in each file. I tried to use "samtool depth", but since the output is so huge - and i need to sum up all the values there, i was wondering of there's a simpler/faster way to get this value.

samtools bedtools RNA-Seq variant calling • 418 views
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It does not make sense to calculate total coverage for each file since regions of your genome may be deeply covered in some places while others may have no reads. If you just need theoretical coverage then you could simply do: (total number of bases sequenced/size of the genome in bases).

You may want to try out mosdepth (LINK) and use one of the coverage options described there in (e.g. specific regions, chromosomes, BED intervals etc).

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