User: shankasal

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shankasal0
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Posts by shankasal

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Answer: A: CQN and EdgeR Library Size for Normalization
... Thanks Aaron, that's a satisfying answer. I had been using the total aligned reads and will continue as such. ...
written 14 months ago by shankasal0
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CQN and EdgeR Library Size for Normalization
... I'm performing quantile normalization with CQN and then using edgeR on some ATAC-seq samples I have and I'm trying to understand/determine the following: When setting the values for library size, Should I use the sum of read counts that fall within the peaks from the total peak (performed for each ...
normalization edger cqn atac-seq written 14 months ago by shankasal0
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Comment: C: Filtering for ATAC-seq
... Thank you both Aaron and Ryan for such detailed responses. I think I understand better now why my current peak calling is not independent of the sample conditions. So if I understand this correctly now, the most appropriate strategy to use for my data set as is would be the following: 1) Pool bam ...
written 14 months ago by shankasal0
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Comment: C: Filtering for ATAC-seq
... So I've tried to look at the Lun and Smyth 2014 Nuc. Acids. Res. paper, and I see from Table 2 that the whole group pooling strategy most closely follows the expected error rate. I don't really understand why though, if it can be explained in layman's terms. Won't a full pooling strategy reduce the ...
written 14 months ago by shankasal0
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Comment: C: Filtering for ATAC-seq
... Thanks for the detailed comment Aaron, I'll ruminate on what you've said. To provide a little more detail on the method I used so far, I called peaks on individual samples and pooled replicates using MACS2 q value 0.01. From there I used IDR to select for and merge peaks between replicates using th ...
written 14 months ago by shankasal0
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Filtering for ATAC-seq
... So I'm trying to determine a couple things when it comes to filtering called peaks that have low read counts relative to the total read counts in all peaks. I'm using the CQN R package to normalize my data set where I currently have 5 cell types with 2 replicates each and analyzing DE peaks with edg ...
edger cqn atac-seq written 14 months ago by shankasal0 • updated 14 months ago by Aaron Lun24k

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