Question: How to create bigwig using mm10.fasta and mm10.fasta bowtie index files
0
gravatar for bioinforesearchquestions
13 months ago by
United States
bioinforesearchquestions200 wrote:

Hi,

I am trying to call copy number from mouse data using HMMcopy.

Created the wig files for my BAM samples. Also created mm10_gc.wig using gcCounter (HMMcopy). I am facing issues while creating the big wig file.

generateMap.pl -w 40 -i mm10 mm10.fa > mm10.bigwig

Getting the following error

HMMcopy_0.1.1/util/mappability/internal/fastaToRead missing, try recompiling...

hmmcopy bigwig wig mouse • 672 views
ADD COMMENTlink modified 13 months ago by ATpoint14k • written 13 months ago by bioinforesearchquestions200
1

It looks like your HMMcopy install is incomplete. Did you compile it yourself? If the said executable (fastaToRead) is there then try adding that directory you $PATH.

ADD REPLYlink modified 13 months ago • written 13 months ago by genomax64k

Hi Genomax, I reinstalled the tool it worked.

ADD REPLYlink modified 13 months ago • written 13 months ago by bioinforesearchquestions200
1
gravatar for ATpoint
13 months ago by
ATpoint14k
Germany
ATpoint14k wrote:

Get kentUtils, and use wigTobigWig. It requires a file with the chromosome sizes, which you can get here. Save the chrSizes as a text file. Then use:

./wigToBigWig in.wig chromSizes.txt out.bigwig
ADD COMMENTlink written 13 months ago by ATpoint14k
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