Question: SAM doubt about sampileup
gravatar for psschlogl
5 weeks ago by
psschlogl20 wrote:

Heu guys I am trying to follow this tutorial:

But at the some point I get stucked. Must of the time I look for some google help or I try untill I got the answer by myself.

But in this part I cant figure out why the this command give a error:

samtools mpileup -f genome/chr22_with_ERCC92.fa.fai -r 22:18918457-18918467 aligns/UHR.bam aligns//HBR.bam
[E::fai_build_core] Format error, unexpected "2" at line 1

I used this command in the fa dir:

samtools faidx chr22_with_ERCC92.fa

and got what I think was the expected fai:

chr22_with_ERCC92.fa  chr22_with_ERCC92.fa.fai

I dont know if I need to put all the necessary files in one dir and do the commands there, but I am wonder why this didnt work if I put the dir/file in the command similar to the tutorial.

Could some of the friends give a direction?


rna-seq sequence • 110 views
ADD COMMENTlink modified 5 weeks ago by Pierre Lindenbaum121k • written 5 weeks ago by psschlogl20
gravatar for Pierre Lindenbaum
5 weeks ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum121k wrote:
-f genome/chr22_with_ERCC92.fa


-f genome/chr22_with_ERCC92.fa.fai
ADD COMMENTlink written 5 weeks ago by Pierre Lindenbaum121k mistake. 8( thanks bro.

ADD REPLYlink written 5 weeks ago by psschlogl20
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 922 users visited in the last hour