uoflbioinformatics/csi-utr

A pipeline for detecting differential expression of 3-prime UTRs

csi-utr's Issues

Hardcoded paths not allowing users to use a different path for bed and annot files

There are a couple arguments that seem to be hardcoded and don't incorporate what the user specifies (i.e. -bed and -annot arguments).

In line 226, https://github.com/UofLBioinformatics/CSI-UTR/blob/master/CSI-UTR_v1.1.0/bin/CSI-UTR, the annotation file is hardcoded to "./data/annotations/$genome.CSIs.annot.bed" whether or not we specify the flag 'annot' with a path.

In line 255, the bed file is hardocded to './data/locations/$genome.CSIs.bed' even though there is a flag to specify the path to the bed file as an argument. Hence similarly, I can't use a different path for the bed file.

When I specify paths for these arguments, I got an error saying the files are not found. My understanding is that because the paths are hardcoded, the tool will always look at ./data/annotations/ folder for these files.

runing CSI-UTR on bam files from STAR using Gencode v27 annotation file

Dear team,

First of all, thank you for this great tool!

I have a paired-end, unstranded RNA-Seq dataset 2 conditions each with 3 replicates. The bam alignment files are generated using STAR with hg38 genome assembly and providing Gencode v27 GTF file. I would like to know if I can use the Hg38.CSIs.bed file in the CSI-UTR-master/CSI_Files/ENSEMBL/Human directory? or should I generate a SCI.bed file for Gencode annotation?

Thank you so much in advance!
Kind regards,
Jamal.

something wrong with Mm10 annotation

Just running CSI-UTR -genome=Mm10, it computes the coverages correctly, but then fails with this:

Annotation for CSI ENSMUSG00000025902:4491716_4490930-4489289 Not defined.  Please check that correct CSI bed file (-bed flag) and annotation file (-annot flag) are used at ../../../../../CSI-UTR-master/CSI-UTR_v1.1.0/bin/CSI-UTR line 1134, <COVERAGE> line 1.