Contamination check errors about irap HOT 4 CLOSED

Hi,
Thank you for the detailed report. In September (version 0.8.5.p3) there was a fix in the invocation of Bowtie - I'm not sure if it would solve the above issue. If you are willing to try please let me know if it continues to fail. I made several changes to the script for the coming 0.9 version which should make the script more robust and flexible. If it is a bowtie bug an alternative is to use bowtie2 by adding
cont_mapper=bowtie2
in the configuration file.
Cheeers.

from irap.

Thanx for the swift reply, as always.

Depending on how our run ends in the next days, we will first test with bowtie2 as the cont_mapper and perhaps then try a newer version.

I was wondering, is there a changelog, I can't find it in the codebase anywhere.. but that could be me.

And one more small question I have: iRAP is aimed at RNAseq but in principle it could be used with DNAseq (using Bowtie or BWA as the mapper), is this recommended or are there really RNA specific steps in the steps that lead to the sorted Bam file?

Looking forward to 0.9,

Highest regards,

Freek.

from irap.

Hi,
There is no changelog, however you may get the list of changes (in the last 6 months) by running
git log --since="6 months ago"
in the cloned iRAP folder.
Yes, in theory iRAP could be used to align DNAseq data. The only step that may be missing is to remove duplicated reads (you may check the fastqc report to see if this is a problem in your data).
Cheers.

from irap.

Hi! In preparation of the coming release (0.9.0) I'm going through all issues. This seems to sorted in the new version - please reopen the issue if necessary. Cheers.

from irap.