Question: SAM doubt about sampileup
0
gravatar for psschlogl
11 months ago by
psschlogl30
psschlogl30 wrote:

Heu guys I am trying to follow this tutorial: https://github.com/griffithlab/rnaseq_tutorial/wiki/PostAlignment-Visualization

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:

ls
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?

Thanks

rna-seq sequence • 232 views
ADD COMMENTlink modified 11 months ago by Pierre Lindenbaum128k • written 11 months ago by psschlogl30
4
gravatar for Pierre Lindenbaum
11 months ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum128k wrote:
-f genome/chr22_with_ERCC92.fa

not

-f genome/chr22_with_ERCC92.fa.fai
ADD COMMENTlink written 11 months ago by Pierre Lindenbaum128k

iuuuu...my mistake. 8( thanks bro.

ADD REPLYlink written 11 months ago by psschlogl30
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