Issue with Thymus ENCODE WGBS Data #108
Description
Hello,
I am currently conducting plasma cfDNA enzymatic methyl-seq analyses related to thymic epithelial tumors. I found ENCODE WGBS data for thymus epithelial cells (https://www.encodeproject.org/experiments/ENCSR914REH/), processed the data using Bismark, generated PAT and BETA files, made an atlas with the ~other 38 HG38 cell types (removed dermal fibroblasts), and successfully detected thymus enrichments in our cfDNA samples compared to controls. However, upon reviewing the atlas itself, the thymus portion has ~3500 NA values out of the 9750 blocks. From the wgbs_tools tutorials, I noticed that the ENCODE thymus data shows up in some of the graphics, but was not in the final atlas. Is something wrong with the original thymus data?
I then looked at NA regions to see what is happening and compared it to other cell types that do not have NA, the thymus data have way fewer cpg sites in the region. I then took the hypomethylated markers for thymus and aligned it with two sets of histone data and saw the enrichments I expected to see. Do you have any thoughts on why the NAs are so high. The final bam has a coverage of ~41X. Thank you!
