Question: Where to find Bowtie2 output stderr filehandle?
0
gravatar for hudiejie
4.1 years ago by
hudiejie20
Singapore
hudiejie20 wrote:

Dear all,

I want to find the alignment rate as suggested in bowtie2 "standard error" ("stderr") file, but after running bowtie2, there is only one bam file of aligned reads. where can I find the info like this:

20000 reads; of these:
20000 (100.00%) were unpaired; of these:
  1247 (6.24%) aligned 0 times
  18739 (93.69%) aligned exactly 1 time
  14 (0.07%) aligned >1 times
93.77% overall alignment rate
bowtie2 • 1.7k views
ADD COMMENTlink modified 4.1 years ago by Bjoern Gruening5.1k • written 4.1 years ago by hudiejie20
1
gravatar for Bjoern Gruening
4.1 years ago by
Bjoern Gruening5.1k
Germany
Bjoern Gruening5.1k wrote:

Hi,

if you click the 'i' symbol you will find a link to stdout and stderr, this will redirect you to the information you need.

Ciao,

Bjoern

ADD COMMENTlink written 4.1 years ago by Bjoern Gruening5.1k

I found it! Thanks a lot!

ADD REPLYlink written 4.1 years ago by hudiejie20
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