Entering edit mode
2.1 years ago
melissachua90
▴
70
I want to find the tradeoffs between using a smaller seed length (12 bases) verses a longer one (40 bases). I don't see any difference in tradeoffs between 12 (53 seconds) and 40 bases (54 seconds). Did I make a mistake? How should I find the tradeoffs?
bowtie -q out1.fq out2.fq -x NC_008253 -l **12** -S -X 600 -t -v 3 > shortmap.sam
bowtie -q out1.fq out2.fq -x NC_008253 -l **40** -S -X 600 -t -v 3 > longmap.sam
smaller seed length:
bowtie -q out1.fq out2.fq -x NC_008253 -l 12 -S -X 600 -t -v 3 > shortmap.sam
Time loading forward index: 00:00:00
Time loading mirror index: 00:00:00
End-to-end 2/3-mismatch full-index search: 00:00:53
# reads processed: 1000000
# reads with at least one alignment: 939659 (93.97%)
# reads that failed to align: 60341 (6.03%)
Reported 939659 alignments
Time searching: 00:00:53
Overall time: 00:00:53
longer seed length:
bowtie -q out1.fq out2.fq -x NC_008253 -l 40 -S -X 600 -t -v 3 > longmap.sam
Time loading forward index: 00:00:00
Time loading mirror index: 00:00:00
End-to-end 2/3-mismatch full-index search: 00:00:54
# reads processed: 1000000
# reads with at least one alignment: 939659 (93.97%)
# reads that failed to align: 60341 (6.03%)
Reported 939659 alignments
Time searching: 00:00:54
Overall time: 00:00:54
Why reason you are changing well-tested defaults? Why do you want to change it?
It was part of an assignment task/question.
Fine, but trade-off for what?