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No. Of Reads & No. Of Bases Per Locus-Calculation

I have RNAseq illumina paired reads mapped to reference genome using bowtie and samtools. I have both bam file and mpileup file. Are there any tools to calculate average number of reads and average number of base pairs for each contig/chromosome?

samtools coverage
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updated by Ram Ram • written by jackuser1979 jackuser1979

do you mean number of reads per region of interest? please do edit your question to be more clear

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written by Rm Rm

1 answer

I'm with Rm, please make your intent more clear. Try:::

~/tools/samtools/samtools flagstat your.bam
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updated by Istvan Albert Istvan Albert • written by Zev.Kronenberg Zev.Kronenberg

Thanks. Now I got it. by samtools idxstats, I got number of basepairs & no.of reads mapped for each contigs.

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written by jackuser1979 jackuser1979

It would be nice to mark it as an answer if it solved your question.

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written by Arun Arun

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