Post Alignment basic QC of RNA-Seq data
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14 months ago
daewowo ▴ 60

I am trying to find a simple way to generate (post alignment) 1) coverage of reference, 2) depth of coverage - either average or running value accross the genome.

I tried GATK DepthOfCoverage but cant work out the --interval parameter.

samtools bamstats gives coverage

Bases mapped: 1,085,991 (97.8%)

Is there a simple tool that can calculate average depth of coverage and eg min depth max depth

alignment RNA-Seq • 412 views
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Entering edit mode
14 months ago

You probably want the percentage of reads assigned to genes. Average coverage would be a silly statistic to work out for RNASeq.

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