.BAM to .BED to Coverage Plots
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5 months ago

Hello all, I have been stumped for a good number of weeks concerning scATAC. For analysis, I ran CellRanger to generate the /outs file which left me with possorted.bam files for each of the 10 samples. After that I ran bedtools bamtobed -I Sample_x_possorted.bam which would generate .bed files; I then ran this through macs2 in order to find peaks (I got .narrowPeaks, and wig files) .

From here, where do I go for analysis?

*Please do not send a link to a vignette as I have already probably read it. I am looking for a succinct explanation for how to analyze from beginning to end from here on out. Thank you.

scATAC-seq Macs scatac signac • 297 views
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Kind of hard to advise without knowing the experiment, what questions you're trying to answer, or what you're trying to accomplish....have you read the literature? Papers such as Assessment of computational methods for the analysis of single-cell ATAC-seq data (Chen et al., 2019) or Comprehensive analysis of single cell ATAC-seq data with SnapATAC (Fang et al., 2021), and followed references in each? There's a ton of information to be had with a few hours of reading that might clear up a good number of week's confusion (hopefully?). Succinct explanations require some kind of foothold. Where are you stuck?

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So I'm stuck after generating the .bed files. Don't know how to create a ChromatinAssay or some sort of object through that in order to generate peaks this way in Signac: https://stuartlab.org/signac/articles/peak_calling.html

After that, where do I proceed from here using the Signac pipeline? I'll take a look at the references, thanks!


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