I am running bowtie on a pair end alignment (illumina hiseq). Here is the command and the output I got:
bowtie -p 4 -v 2 -k 11 -m 10 -t --best /bowtie/indexes/hg19 -1 /data/rna_seq/0916_1.fq -2 /data/rna_seq/0916_2.fq /data/rna_seq/0916.SAM -S
Time loading forward index: 00:00:08
Time loading mirror index: 00:00:08
Time loading reference: 00:00:03
End-to-end 2/3-mismatch full-index search: 04:48:55
# reads processed: 114497412
# reads with at least one reported alignment: 64037326 (55.93%)
# reads that failed to align: 50290127 (43.92%)
# reads with alignments suppressed due to -m: 169959 (0.15%)
Reported 94715801 paired-end alignments to 1 output stream(s)
Time searching: 04:49:14
Overall time: 04:49:14
Time loading forward index: 00:00:08
Time loading mirror index: 00:00:08
Time loading reference: 00:00:03
End-to-end 2/3-mismatch full-index search: 04:48:55
# reads processed: 114497412
# reads with at least one reported alignment: 64037326 (55.93%)
# reads that failed to align: 50290127 (43.92%)
# reads with alignments suppressed due to -m: 169959 (0.15%)
Reported 94715801 paired-end alignments to 1 output stream(s)
Time searching: 04:49:14
Overall time: 04:49:14
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