Checking sex of a sample with sequencing data

Question

[xqyn]

Hi everyone,

I have a set of FASTQ files from an ATAC-seq experiment. After mapping, I generated BAM files. Is there a way to determine the sex of the samples based on these BAM files?

Thanks!

[ATpoint]

Checking whether you have signal on chrY would be a good start. That said, how can it be that you have data without info on the underlying experiment including the sex? That are key metadata that need to be documented.

[xqyn]

Yes, I have checked the signal on chrY data. The problem is that the sample have the peak signals for chrY in ATAC-seq data; however, it also contains signal for X-linked chromosome like XIST genes.

[ATpoint]

So you mean you see peaks at Xist which makes you think it's activate X-inactivation, hence its female? Can you show some plots or anything?

[xqyn]

can you give any thought? (scale:0-2000)