I get this warnings sometimes when I run bw_bins using hg_38 on our bigWig files. The reason for this is most likely that reference hg38 version used to map the reads is not the same as the one provided by BSgenome.Hsapiens.UCSC.hg38, which is GRCh38.p12.
Results-wise it does not seem extremely relevant for the bins analysis, since main chromosome sequences are the same, but there are a few region patches that are not found in the reference we have. Possible solutions are mapping to the same versions of hg38 or use only main chromosomes for our analysis and filter out all non-localized, fixes and novel patches before summarizing bigWig files, which I think it's the cleanest.
I get this warnings sometimes when I run
bw_binsusinghg_38on our bigWig files. The reason for this is most likely that referencehg38version used to map the reads is not the same as the one provided byBSgenome.Hsapiens.UCSC.hg38, which isGRCh38.p12.Results-wise it does not seem extremely relevant for the bins analysis, since main chromosome sequences are the same, but there are a few region patches that are not found in the reference we have. Possible solutions are mapping to the same versions of
hg38or use only main chromosomes for our analysis and filter out all non-localized, fixes and novel patches before summarizing bigWig files, which I think it's the cleanest.