Question: SAM doubt about sampileup
gravatar for psschlogl
11 months ago by
psschlogl30 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 • 232 views
ADD COMMENTlink modified 11 months ago by Pierre Lindenbaum128k • written 11 months ago by psschlogl30
gravatar for Pierre Lindenbaum
11 months ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum128k wrote:
-f genome/chr22_with_ERCC92.fa


-f genome/chr22_with_ERCC92.fa.fai
ADD COMMENTlink written 11 months ago by Pierre Lindenbaum128k mistake. 8( thanks bro.

ADD REPLYlink written 11 months ago by psschlogl30
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: 1240 users visited in the last hour