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Old 04-22-2015, 01:54 AM   #8
Location: Uganda

Join Date: Jan 2015
Posts: 71

Originally Posted by Michael.Ante View Post
You can download the virus sequences in fasta format and use e.g. Bowtie2 to align the reads locally. Therefore, you need to build an index first. The log output of Bowtie2 tells you haw many reads mapped.
After aligning the reads, you can use samtools to get some statistics (e.g. samtools idxstats).
Hello Michael, when I try samtools idxstats,
I am getting a comment as below;

samtools idxstats lib4seq.sorted.bam
[bam_idxstats] fail to load the index.

what could be the problem?
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