TCGA Wiggle files for MuSiC

Question

[TriS]

hi all

I am working with somatic mutations in prostate, I downloaded the MAF files + clinical data from TCGA and I installed MuSiC to work with them...however, I need bam or wig files. since I have no access to the bam files, I would like to get hold of the Wiggle files but I am not really sure where to find them/which ones to use...

also, wig files are still pretty big guys (i.e. wiggle files for some ChIPSeq data I worked with are >200Mb each...) ...so if I need to download 200Mb x 400 patients that's gonna be pretty challenging..any suggestions how to circumvent that?

any help would be great.

thanks

[nnutter]

I don't think you've left enough information in your question for anyone to be able to offer advice. I suspect the answer will be along the lines of how to automate downloading those 400 files. It's definitely a skill worth investing time in.

[TriS]

@nnutter - tnx for the reply, I'm actually ok on how to automate the download of lots of files, I simply don't know where to find them!

so, if it clarifies it a lil, I don't know which Wiggle files I need to use with MuSiC for the "clinical-correlation" and "survival" functions and, not knowing which Wiggle files to use, i don't really know where to get them from.

Answer 1

[Cyriac Kandoth]

Wiggle files contain coverage status per bp, that some TCGA GSCs like Broad upload within their MAF archives. So for TCGA PRAD, you'll find them here.

~2 years ago, I had tried to systematically collect coverage data across TCGA exome-seq. It doesn't include a lot of the newer data. But all my notes are now belong to you: http://dx.doi.org/10.7303/syn1695394

[TriS]

that's exactly what I needed to know.

thanks :)