search

BenoitCastandet / chloroseq

a bioinformatic pipeline to systematically analyse the chloroplast transcriptome using RNA-Seq
6 stars 4 forks source link

Editing analysis #3

Open benjaminlenzen opened 5 years ago

benjaminlenzen commented 5 years ago

Hi there,

I was running the pipeline successfully on some plastid RNAseq data. But couldn't get any output for the editing analysis. Could that be caused by an version conflict with samtools? The mpileup file is created and around 800mb big. But then the pipeline dies with this error statement:

Starting editing analysis (Analysis 3). [mpileup] 1 samples in 1 input files

Set max per-file depth to 8000 Indel size not accounted for Any suggestions? Best, Ben
BenoitCastandet commented 5 years ago

Hi Ben

This message happens when there are indels as the script doesn't deal with them. What version of samtools are you using? Briefly looking at the releases it seems to me that the newer versions don't use the -I option the same way. It might be the reason although i'm not sure.

When you look at the pileup file, do you have the editing snp at the right spots?

Best

Benoît