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?