Question: How to Separate a SAM File Containing Forward and Reverse Reads
16 months ago by
Ric • 290
Ric • 290 wrote:
I got 0 plus and minus reads by aligning single reads against a gene in the following way:
> bwa index ref.fasta > bwa mem ref.fasta sample5-21.fq | gzip -3 > sample5-21.sam.gz > splitsam.sh sample5-21.sam.gz forward.sam.gz reverse.sam.gz Total reads: 1792444 Plus reads: 0 Minus reads: 0 Unmapped reads: 1792444 Time: 1.166 seconds.
What did I miss?
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