No. Of Reads & No. Of Bases Per Locus-Calculation
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12.1 years ago
jackuser1979 ▴ 890

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 • 3.7k views
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do you mean number of reads per region of interest? please do edit your question to be more clear

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12.1 years ago

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

~/tools/samtools/samtools flagstat your.bam
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Thanks. Now I got it. by samtools idxstats, I got number of basepairs & no.of reads mapped for each contigs.

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

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