Hi Galaxy Developers,
Note, meta-feature = gene and feature = exon.
I need your help with incorporating a feature into the galaxy tool wrapper for a particular tool and update in the tool shed, so that galaxy administrators can install a new version.
Specifically, there is an option missing from the featurecounts tool (all available versions are the same), is it possible to update the tool?
The option I am referring to is assigning a fraction to “allow reads to contribute to multiple features (-O)”. In the featurecounts manual, found on the wehi website (http://bioinf.wehi.edu.au/featureCounts/) you can assign a fraction for reads that contribute to multiple features, however this is not an option in the galaxy version of the tool (skip to section 6.2.6 of the manual). Without this fraction option, a “multioverlapping” read that maps an exon-exon junction, or to an exon shared between genes, is counted twice, once for each feature.
I can only specify to count or discard these reads (with yes or no respectively), but it would be better to be able to divide the read count by the number of features that read maps to.
Ideally, this option would be set up the same as for the “count multi-mapping reads/fragments” option, with a drop down menu that when you choose enabled, then another option pops up to allow a fraction to be calculated.
The distinction between multioverlapping and multimapping reads is important, the multimapping reads are ambiguously mapped whereas the multioverlapping reads are mapped confidently. Adding a fraction option would vastly improve exon-level expression estimation, since counting a read twice just because it overlaps features over-estimates exon-level expression compared to gene-expression, where a read is just counted once for the gene regardless of whether it crosses an exon-exon border.
I hope this all made sense,
Thank you for your time,