hello, i am running gsnap with rna seq data against a reference genome:
gsnap -m 10 -B 5 -t 8 -A sam -d GENOME seqs.fastq > res.sam
but strangely, the output sam file contains more reads than the original fastq files:
$ cat seqs.fastq | echo $((`wc -l`/4))
3776979
$ cat res.sam | grep -v '^ *@' | wc -l
6009141
and I don't understand what that means....
thank you
gsnap -m 10 -B 5 -t 8 -A sam -d GENOME seqs.fastq > res.sam
but strangely, the output sam file contains more reads than the original fastq files:
$ cat seqs.fastq | echo $((`wc -l`/4))
3776979
$ cat res.sam | grep -v '^ *@' | wc -l
6009141
and I don't understand what that means....
thank you
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