<p>hi all</p>

<p>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...</p>

<p>also, wig files are still pretty big guys (i.e. wiggle files for some ChIPSeq data I worked with are &gt;200Mb each...) ...so if I need to download 200Mb x 400 patients that&#39;s gonna be pretty challenging..any suggestions how to circumvent that?</p>

<p>any help would be great.</p>

<p>thanks</p>

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][1].

~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

 [1]: https://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/prad/gsc/broad.mit.edu/illuminaga_dnaseq_curated/mutations/broad.mit.edu_PRAD.IlluminaGA_DNASeq_curated.Level_2.1.4.0/