nellore / region_matrix Goto Github PK

I'm using sorted BAM files that have numeric chromosome names (no "chr" prefix). There seems to be an issue with quantification. If I remove "chr" from your degradation BED file chromosome names, I get 0's for quantification of regions on chromosomes 10-19.

If I sort the BED file so that numeric chromosomes are in numeric order (to match BAM files), I get the following error I think from wiggleTools:
"Position 10:714133 is before 9:140899137"
even though the BED file looks like

9	140049063	140050870	.	0	.
9	140791269	140791603	.	0	.
9	140833366	140833967	.	0	.
9	140899136	140899908	.	0	.
10	714132	714671	.	0	.
10	7830132	7830226	.	0	.
10	51565182	51565296	.	0	.
10	51580555	51580696	.	0	.
10	51632928	51633033	.	0	.
10	60028911	60029064	.	0	.