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Old 04-23-2015, 05:43 AM   #11
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).
In a case where my index file has several sequences for different strains/isolates of the same virus which may be treated as duplicates, how do I restrict bowtie2 to do the alignment once?
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