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

Question

[jackuser1979]

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?

[Rm]

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

Answer 1

[Zev.Kronenberg]

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

~/tools/samtools/samtools flagstat your.bam

[jackuser1979]

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

[Arun]

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