Question: -N and -L in bowtie2
0
gravatar for A
4.6 years ago by
A3.7k
A3.7k wrote:

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

mismatch seed bowtie2 • 1.2k views
ADD COMMENTlink modified 4.6 years ago by Devon Ryan94k • written 4.6 years ago by A3.7k
2
gravatar for Devon Ryan
4.6 years ago by
Devon Ryan94k
Freiburg, Germany
Devon Ryan94k wrote:

-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!

ADD COMMENTlink written 4.6 years ago by Devon Ryan94k

thank you Devon

 actually my adviser asked me to do like this..im too new yet and i cant get the reason of these arguments...

ADD REPLYlink written 4.6 years ago by A3.7k
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