Question: How To 'Genome Music Play' Using Wig File Instead Of Bam File?
3
gravatar for jessada115
6.0 years ago by
jessada11540
jessada11540 wrote:

Can you please guide me how to solve this problem? I'd like to use TCGA data as MuSiC input but don't have controlled-access at a moment. This means that I can't use BAM file as MuSiC input. Do you have any suggestion to circumvent this problem to run 'genome music play'? From the installation guide at Installation of the MuSiC suite on unsupported linux distributions, it suggest using wig file to replace BAM file but it didn't explain how to plug this replacement in 'genome music play'.

Do I have to create my own pipeline? Or I can just need to add a few more parameters to indicate wig file in 'music play'?

bam music • 2.2k views
ADD COMMENTlink modified 6.0 years ago by mdm-two230 • written 6.0 years ago by jessada11540
4
gravatar for mdm-two
6.0 years ago by
mdm-two230
mdm-two230 wrote:

I think you will need to use music bmr calc-wig-covg to generate the gene coverage files.

ADD COMMENTlink modified 6.0 years ago by Istvan Albert ♦♦ 81k • written 6.0 years ago by mdm-two230
2

This is correct. The "music play" script only works with "music bmr calc-covg" that requires BAM files. If you only have access to wig files, you will need to run "bmr calc-wig-covg", followed by "bmr calc-bmr", and then the "smg" test and other MuSiC modules.

ADD REPLYlink written 6.0 years ago by Cyriac Kandoth5.3k

Short follow-up question, in the specification for bmr calc-bmr you have to have list of bam files. I only have wig files no bam files. I did the calc-wig-covg, should I use the outputfiles from that analysis instead somehow? (Sorry if I'm missing something obvious)

ADD REPLYlink written 5.9 years ago by Matilda0

Yes, calc-wig-covg generates a gene_covgs directory and a file named total_covgs which is all the information needed by calc-bmr... which is the necessary next step of either calc-covg or calc-wig-covg.

ADD REPLYlink written 5.9 years ago by Cyriac Kandoth5.3k
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