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entropy vs sequencing depth/CG content #214
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Hello @ywang285, If you don't have deep enough coverage to sample all of I have less of an intuition for how CpG density will change entropy. Given a constant number of CpGs ( So in general, I would recommend trying to get as high coverage as possible (to a point, 30X/haplotype), and trying multiple settings for |
Thank you so much for your reply! I plan to compare the entropy of genomic regions without amplification (10X-20X depth) vs. amplicon regions (>100X depth). However, it sounds that the comparison won't be fair unless I subsample the amplicon region. Is that the case or if you have any suggestions? |
Hello @ywang285, I don't think you'll need to sub-sample the amplified reads since they should have very low modification rates. If there is high native methylation entropy in a genomic region it should be noticeable above an amplified background. |
Hi, Thank you for providing this great tool! I am interested in calculating CpG entropy, and I am wondering how sequencing depth (such as comparing data with 10X coverage vs. 30X coverage) and CG content (e.g., comparing reads from high CG content region and low CG content region but still have >=4 CG in the window size) affect entropy value. Thank you!
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