Question: MuSiC original files for testing/ MAF, rois and soo on
1
gravatar for uscUserMut
21 months ago by
uscUserMut10
Germany
uscUserMut10 wrote:

hi all,

i'm new and interested to test music v0.4 . now i have problems to get the same result like in the paper (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3409272/)

"MuSiC: identifying mutational significance in cancer genomes.Dees ND1, Zhang Q, Kandoth C, Wendl MC, Schierding W, Koboldt DC, Mooney TB, Callaway MB, Dooling D, Mardis ER, Wilson RK, Ding L."

 

i downloaded, the same files like it's noticed in the paper:

<"Sample data set used in this study

<Alignment mapping files for the ovarian cancer cohort, as well as all mutational data in mutation annotation format <(MAF) are available at The Cancer Genome Atlas (TCGA) website, http://cancergenome.nih.gov/, via dbGaP. The <dbGaP study accession number is phs000178.v1.p1. "

But anyway. no chance to get the same results. i have the oppertunities or  access to get all data, i hopefully think ;) , but it doesn't work.

Could anyone help me with the original files or  links directly to the original files from that paper?

with best regards

max

 

sequencing music genome • 722 views
ADD COMMENTlink modified 21 months ago by Cyriac Kandoth4.6k • written 21 months ago by uscUserMut10

Can you list out the exact data you are using? And which tools in the MuSiC suite are you trying to perform? In "Installation of the MuSiC suite on unsupported Linux distributions" I provide a list of "Datafiles and sample inputs".

ADD REPLYlink written 21 months ago by Cyriac Kandoth4.6k

at first thanks! i will post it the next days.

ADD REPLYlink written 21 months ago by uscUserMut10
3
gravatar for Cyriac Kandoth
21 months ago by
Cyriac Kandoth4.6k
Memorial Sloan Kettering, New York, USA
Cyriac Kandoth4.6k wrote:

A lot has happened since that publication, so here is an updated list of links to the data used.

Mutations from 316 TCGA OV (ovarian cancer) samples in Mutation Annotation Format (MAF) is from this TCGA publication. To avoid Excel spreadsheet related problems, use the plain-text OV MAF downloadable here.

Alignment mapping (BAM) files are best downloaded from CGHubIf you don't have access to CGHub, it might be simpler to use bmr calc-wig-covg in place of bmr calc-covg. Wiggle files can be found in the Mutation_Packager_Coverage archive from Firehose.

Sample ROI files for use with bmr calc-covg and bmr calc-bmr, can be found in the calc-roi-covg repo.

The datafiles used by MuSiC's cosmic-omim and pfam tools are downloadable from here.

ADD COMMENTlink written 21 months ago by Cyriac Kandoth4.6k
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