Closed sr320 closed 4 years ago
@yaaminiv here are the bed files:
Mcap:
Pact:
you could also run the following code to download them if that's easier:
wget -r \
--no-directories --no-parent --reject "index.html*" \
-P . \
-A CpGs.bed https://gannet.fish.washington.edu/metacarcinus/FROGER_meth_compare/20200504/data/Mcap/
wget -r \
--no-directories --no-parent --reject "index.html*" \
-P . \
-A CpGs.bed https://gannet.fish.washington.edu/metacarcinus/FROGER_meth_compare/20200504/data/Pact/
The columns are the same as the union bed file so there are more than 4 columns, but I don't think it should affect bedtools intersect because the first 3 columns are still:
jupyter notebook used to create files is here: https://github.com/hputnam/Meth_Compare/blob/master/scripts/Generate_UpsetPlot_input.ipynb
@yaaminiv NOTE: these files do not contain redundant CpGs. In other words, if a CpG is listed in one file, it is not listed in any other file.
I identified genomic location in this script and reformatted tables/created plots in this R Markdown.
(from bottom to top of each bar: CDS, introns, flanks, intergenic)
(from bottom to top of each bar: CDS, introns, flanks, intergenic)
Will tackle stats next
This is in relation to "upset" plot discussion today.
Approach / downstream wise I would suggest taking the union bedgraph and simply parsing based on approaches covering loci, recalling that in our conversation we stated only one sample per method would count.
Resulting bed files would then easily go to Yaamini for feature analysis.
should be ~ 8 files?
MBD - WGBS - RRBS MBD - WGBS MBD - RRBS WGBS - RRBS WGBS only MBD only RRBS only None