SAM doubt about sampileup

Question

[psschlogl]

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

Answer 1

[Pierre Lindenbaum]

-f genome/chr22_with_ERCC92.fa

not

-f genome/chr22_with_ERCC92.fa.fai

[psschlogl]

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