-N and -L in bowtie2

Question

[zizigolu]

Sorry friends,

I used the below syntax but the result seems strange for me, what is the reason please

bowtie2 -x [name] -N 0 -L 15 -U [file_trimmed.fastq -S file.sam

[izadi@lbox161 ~]$ bash
[izadi@lbox161 ~]$ cd /usr/data/nfs6/izadi/project
[izadi@lbox161 project]$ export BT2=/usr/people/home/izadi/fereshteh/bowtie2-2.2.5
[izadi@lbox161 project]$ echo $BT2
/usr/people/home/izadi/fereshteh/bowtie2-2.2.5
[izadi@lbox161 project]$ $BT2/bowtie2 -N 0 -L 15 -x rRNA --un SRR1211041_trimmed_unmapped.fastq -U SRR1211041_trimmed_unmapped.fastq -S mapped_and_unmapped.sam
0 reads
0.00% overall alignment rate

Answer 1

[Devon Ryan]

-N 0 is the default, so you needn't specify it unless you're changing things. Often as -L is decreased you need to increase -D as well, so try the defaults and see if they produce any alignments and then tweak from there.

Also, you really don't want to give the same file to --un and -U. You'll end up over writing the file you're trying to align!

[zizigolu]

Thank you Devon

Actually my adviser asked me to do like this. I'm too new yet and I can't get the reason of these arguments.