RNA-SeQC v1.1.7 05/14/12
Creating rRNA Interval List based on given GTF annotations
RNA-SeQC Total Runtime: 0 min
Sample File: tab-delimited description of samples and their bams. This file header is:
Sample ID Bam File Notes
When running on just one sample, this argument can be a string of the form
"Sample ID|Bam File|Notes", where Bam File is the path to the input file.
I got it all working by reverting back to assembly and annotation Ensembl 37. I did source my fasta and gtf files from GENCODE, but I think it didn't matter in the end, as long as I used other assembly, not the latest one. I'm pretty sure RNA-SeQC breaks when the latest assembly - Ensembl 38 used, as it was build when Ensembl 37 was the latest, but the gtf format has changed in Ensembl 38. I raised an issue on github RNA-SeQC error no output , but it doesn't look they check they page. I wanted to write to them directly, but couldn't find the best email to contact.
If you or anyone else knows the best contact email regarding RNA-SeQC please let me know. And also if you or anyone else have any thoughts on RNA-SeQC not working with the latest assembly - Ensembl 38, please comment on github issue page or here.