Entering edit mode
8.6 years ago
fabio.liberante
▴
30
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!
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 usingsed "s/^chr//" hg38.HouseKeepingGenes.bed > hg38.HouseKeepingGenes.nochr.bed