Clipper with non model organisms

[matthew-valentine]

I have been trying to use clipper with a custom annotation (hg38 plus additional over expressed genes) but I am unable to get it to work. In the wiki it mentions that when not using a model organism you can forgo the -s option in favour of using a custom gene definition file by calling the --bedFile option. However, this doesn't actually appear to be an option in the version I just downloaded (v 0.1.4). Is there currently a way to use clipper for data not mapped to hg19 or mm9? I noticed that other people have mentioned this problem (e.g. issue #54) but there doesn't seem to be any advice on what to do in this situation.

Thanks in advance for any help you can give!

[byee4]

While we're still using Clipper for our model organisms, the graduate student who maintained this code has left some time ago. I believe that this --bedFile option doesn't quite work, but I think you can include custom BED and a GTF-like AS.STRUCTURE file (see below examples) inside clipper/data/regions before running the install. I think you can get away with including two files (you might need a _genes.bed file too, but I don't think so):

Here is an example of a custom annotation (hg19 + additional sequences) that appears to work, that you can use as an example:

https://github.com/YeoLab/clipper/blob/master/clipper/data/regions/hg19_VSV_exons.bed
https://github.com/YeoLab/clipper/blob/master/clipper/data/hg19_VSV.AS.STRUCTURE.COMPILED.gff

[matthew-valentine]

Thank you so much for the response. I was working on some other projects for a while but now I am back on this one. How would you go about calling these files as part of the clipper pipeline? From what I can see in the options, beyond -s there are no options for specifically calling any exon or structure files.

[byee4]

i think -s will just look in that data/ folder for the given prefix, so in that example, you would specify

-s hg19_VSV

which will look for:

data/regions/hg19_VSV_exons.bed
data/hg19_VSV.AS.STRUCTURE.COMPILED.gff