Entering edit mode
8.7 years ago
zizigolu
★
4.3k
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
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.