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Old 10-15-2011, 06:24 AM   #1
Location: Seattle

Join Date: Jul 2011
Posts: 98
Default Can GSNAP generate SAM/BAM files?

I am running gsnap with this command:

gsnap --gunzip -d Drosophila5 -D /home/efoss/gene_databases/GMAP_GSNAP_db/ D09NJACXX_s8_1_illumina12index_8_SL7777.fastq.gz D09NJACXX_s8_2_illumina12index_8_SL7777.fastq.gz > D09NJACXX_s8_illumina12index_8_SL7777.sam

The output clearly is not in standard sam format. Is it possible to generate standard sam/bam files with gsnap, and if so, how?

Thank you.

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