Hi Everyone,
I want to use bowtie 1 with such parameters
command 1 : -a -m 5 --best
I went through the manual and it explained the situation where these options were used
command 2 : -a -m 5 --best --strata
I want to know what difference would command 1 give than command 2. Manual explained the output of -a -m 5 --best --strata
. I want to know what would be the output with -a -m 5 --best
(no --strata
used).
I ran the 2 commands with exact values but one included --strata
and other did not. This was the outcome.
-a --best
and --strata -m 10
# reads processed: 7919843
# reads with at least one reported alignment: 163241 (2.06%)
# reads that failed to align: 7733095 (97.64%)
# reads with alignments suppressed due to -m: 23507 (0.30%)
Reported 323300 alignments to 1 output stream(s)
-a --best
and -m 10
(no --strata
option used)
# reads processed: 7919843
# reads with at least one reported alignment: 152085 (1.92%)
# reads that failed to align: 7733095 (97.64%)
# reads with alignments suppressed due to -m: 34663 (0.44%)
Reported 402672 alignments to 1 output stream(s)
Hope to hear soon.
Thanks in advance
Regards
Varun
With such poor alignment my guess is that you have either; untrimmed adapter sequences, messed up paired end sequence files, have sequences contaminants or are searching against the wrong species. FASTQC may help narrow this down, as would a blast search against genbank for a handful of sequences.