FAQ

1. How to create a "contamination" database?

A full example is provided in the examples folder (you may also see the file http://code.google.com/p/irap/source/browse/examples/ex_add2contaminationDB.sh here).

2. How do I specify that I have technical replicates?

Through the "technical.replicates" parameter. Technical replicates are provided together separated by a comma, and biological replicates are separated by a semi-colon. For instance, the following line technical.replicates="s1,s2;s3;s4" indicates that in a data set with 4 samples (designated as s1, s2, s3,and s4), there are three biological samples, and s1 and s2 are technical replicates.

3. I get "ERROR: GTF file contains XXXX comments (lines starting with #). This will break some scripts.", what shall I do?

The conservative approach is to remove all lines starting with # from the GTF.