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How to create bigwig using mm10.fasta and mm10.fasta bowtie index files

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...

bigwig wig mouse hmmcopy
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updated by elbakri.fatimazahrae • elbakri.fatimazahrae • written by bioinforesearchquestions bioinforesearchquestions

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.

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written by GenoMax GenoMax

I get the same error, I reinstalled and recompiling but still have the same error how should I fix it ?!

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written by elbakri.fatimazahrae • elbakri.fatimazahrae

the error is 

src/util/mappability/internal/fastaToRead missing, try recompiling..., getting after the following CMD rc/util/mappability/generateMap.pl  -w 35  -i /Users/mac/Desktop/NGS-/TriTrypDB-47_LmajorLV39c5_Genome.fasta > /Users/mac/Desktop/NGS-/TriTrypDB-47_LmajorLV39c5_Genome-map.bigwig
for compiling i'm using $make -->  2%] Built target split
[ 32%] Built target bamtools
[ 35%] Built target readCounter
[ 72%] Built target kent
[ 75%] Built target mapCounter
[ 77%] Built target fastahack
[ 80%] Built target gcCounter
[ 82%] Built target segToGc
[ 85%] Built target segToMap
[ 87%] Built target bigWigInfo
[ 90%] Built target bigWigToWig
[ 92%] Built target bigWigToBedGraph
[ 95%] Built target bigWigSummary
[ 97%] Built target fastaToRead
[100%] Built target wigToBigWig

? how should I fix it

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updated by ATpoint ATpoint • written by elbakri.fatimazahrae • elbakri.fatimazahrae

I was running the generatemap.pl CMd : util/mappability/generateMap.pl -w 35 -i /Users/mac/Desktop/NGS-/TriTrypDB-47_LmajorLV39c5_Genome.fasta > /Users/mac/Desktop/NGS-/TriTrypDB-47_LmajorLV39c5_Genome-map.bigwig but I get un error : Can't exec "bowtie": Not a directory at util/mappability/generateMap.pl line 105. bowtie not found, obtain from http://bowtie-bio.sourceforge.net/index.shtml and/or add to $PATH how should I fix it. N.B: i was getting bowtie from source , then I get the Path on HMMcopy and I fix on bash_profile. !!

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written by elbakri.fatimazahrae • elbakri.fatimazahrae

1 answer

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
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written by ATpoint ATpoint

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