RSeQC - geneBody_coverage.py - Cannot get coverage signal from ... bam !

Question

[fabio.liberante]

I have successfully installed RSeQC and python -c ‘from qcmodule import SAM’ runs without error. I have tried the following command on a sorted and indexed bam file output from STAR aligner and indexed with samtools.

geneBody_coverage.py -r hg38.HouseKeepingGenes.bed -i Aligned.sortedByCoord.out.bam -o coverage

However, I get the following error

@ 2016-03-14 12:58:26: Read BED file (reference gene model) ...
@ 2016-03-14 12:58:27: Total 3802 transcripts loaded
@ 2016-03-14 12:58:27: Get BAM file(s) ...
        Aligned.sortedByCoord.out.bam
@ 2016-03-14 12:58:27: Processing Aligned.sortedByCoord.out.bam ...

Cannot get coverage signal from Aligned.sortedByCoord.out.bam ! Skip



        Sample  Skewness
@ 2016-03-14 12:58:27: Running R script ...
null device
          1

I checked the bam file with samtools quickcheck and I get no errors. Any help is appreciated!

Answer 1

[GenoMax]

Are the chromosome names matching in the bed/bam file?

[fabio.liberante]

Thanks! That was the problem. I had presumed that — as I used an index and annotation file that had the chr prefix during the STAR alignment — the output BAM would have the chr prefix. I just removed the chr prefix in the bed file using sed "s/^chr//" hg38.HouseKeepingGenes.bed > hg38.HouseKeepingGenes.nochr.bed