The usual hack is 'samtools view file.bam | cut -f 1 | sort | uniq -c'.
If on Windows, you're on your own.
- tom blackwell -
On Tue, 27 May 2014, Lana Schaffer wrote:
> Hi,
> I am aligning to fasta DB of sequences and would like to count
> The number of reads to each fasta entry by header names.
> How do I designate to bowtie to store the names in the SAM
> File and then use samtool to count them?
>
> Lana Schaffer
> The Scripps Research Institute
> Biostatistics, Informatics
> DNA Array Core Facility
> 858-784-2263
>
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