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?
do you mean number of reads per region of interest? please do edit your question to be more clear
I'm with Rm, please make your intent more clear. Try:::
~/tools/samtools/samtools flagstat your.bam
Thanks. Now I got it. by samtools idxstats, I got number of basepairs & no.of reads mapped for each contigs.
It would be nice to mark it as an answer if it solved your question.
Login before adding your answer.
Use of this site constitutes acceptance of our User Agreement and Privacy