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.
Eric
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.
Eric
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