I am working with a paired-end data set of rhesus macaque reads aligned with STAR against a current rhesus .fasta reference and .gtf annotation. I am interested in doing some quality control measures on my .bam file with RNAseqC to determine numbers of reads that map to non-genic, exonic, or intronic regions.
For now, I'm trying to bypass the command-line execution and opting to perform the run on the web-based GenePattern interface offered by Broad institute. For those familiar, there are a number of inputs required for RNAseqC, all of which I believe that I have provided:
-indexed .bam with read groups created with Picard tools -.gtf file -indexed .fasta -dictionary of .fasta created with Picard tools
Unfortunately there is no accompanying 18S rRNA information for rhesus I am able to provide.
Anyways, the program seems to complete successfully, however for all of my transcripts I get this message in the output:
WARNING: Transcript has no coverage: ACTB_transcript_01
This is peculiar to me, because if I load the .bam, .gtf, and .fasta in IGV, there are clearly an abundant number of reads mapping to the ACTB gene.
I am wondering why RNAseqC is not picking up any reads to exons, or anything really. If anyone has encountered similar issues it would be greatly appreciated. From what I have seen, the chromosomes are annotated the same in both the .gtf and .bam file.