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