Bins for chrY are missing

[alexvasilikop]

Hello,

I used the bin annotations for hg38 but I realized that in the segmented file from QDNAseq, part of the Y chr is missing (I am including sex chromosomes in the analyses).

In hg38 the length of Y is 57,227,415 bp.

But my segmented file from QDNAseq file ends like this meaning that only bins up to 26.7Mb (half the chr) are shown:

Y	25900000	26000000	Y:25900001-26000000	-7.033	+
Y	26000000	26100000	Y:26000001-26100000	-7.033	+
Y	26100000	26200000	Y:26100001-26200000	-7.033	+
Y	26200000	26300000	Y:26200001-26300000	-7.033	+
Y	26300000	26400000	Y:26300001-26400000	-7.033	+
Y	26400000	26500000	Y:26400001-26500000	-7.033	+
Y	26500000	26600000	Y:26500001-26600000	-7.033	+
Y	26600000	26700000	Y:26600001-26700000	-7.033	+

What is the issue? I thought there are no blacklisted regions for sex chrs.

Thanks
Alex

[asntech]

@alexvasilikop, apologies for the late response. For some reason I've missed the email notifications.

There are regions from sex chrs in the ENCODE problematic regions.

Can you please give a try to the updated version in the dev branch as this has the recent v2 of the regions from ENCODE?

remotes::install_github("asntech/QDNAseq.hg38@dev")