Why are there no peaks for Y chromosome in ATAC-seq?
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8 weeks ago
Lord.Mor • 0

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.

ATAC-seq Y Chromosome • 382 views
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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.

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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.

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8 weeks ago
Alex ▴ 10

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.

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

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

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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.