Why are there no peaks for Y chromosome in ATAC-seq?

Question

[Lord.Mor]

Hi! This was my first to do the ATAC-seq on a cell culture (which is from a 19-year old male individual). However, after data analysis, there are no peaks for the Y chromosome. Is there any possible explanation for that? I was assuming or expecting that there would be some peaks for chromosome Y because the cells are from a male donor.

Thank you very much in advance for the help and input.

[ATpoint]

This cannot be answered. You would need to add at least some code or a reference to the pipeline you use. Are there no reads at all or just no peaks. Look at the file in a genome browser, maybe the pipeline removed chrY.

[Lord.Mor]

For all the samples (1st and 2nd), there are reads that aligned to the chr Y but no peaks. What's even weirder is that I got a lot of peaks for the samples that came from a female donor.

Answer 1

[Alex]

What did you use to run the data? The pipeline may have removed chr Y prior to, or after alignment.

If that is not the case, a quick test would be to take the BAM file of the replicate and filter for chr Y:

​samtools view -b atac.bam chrY > atac_chrY.bam

Then, take a look at the size. If it isn't 0 bytes, then you have some reads there. Why they are not showing up as peaks could then be for other reasons.

[ATpoint]

samtools idxstats your.bam will easily tell the number of alignments to chrY.

[Lord.Mor]

Yes ATpoint, I used samtools idxstats to check the number of alignments per chromosome. Thanks

[Lord.Mor]

Sorry for the late response. I used the GALAXY online platform (Bowtie2).

I think it is because of other reasons because when I analyzed my second batch of samples, I got peaks for chr Y. What was weirder is that I got peaks for chr Y even if the sample is from a female donor.