Problems converting wig to bigwg

[António Miguel de Jesus Domingues]

Hi Genomers,

I am trying to convert wig.gz files (from QuEST chip-seq analysis) with the tool wigToBigWig. Initially the chromosome sizes were obtained with:
fetchChromSizes hg19 > hg19.chrom.sizes

But then I've ran into problems in the conversion to bigWig:
wigToBigWig background_unnormalized.profile.wig.gz hg19.chrom.sizes background_unnormalized.profile.bw

hashMustFindVal: '1' not found
gzip: stdout: Broken pipe
process exited with 1: "gzip -dc" in pipeline "gzip -dc"

The only source of the problem that comes to my mind is that the reference genome for the the mapping and peak calling was from Ensembl, but this is a wild guess. Could you please help me with this?

Cheers,
António
--
--
António Miguel de Jesus Domingues, PhD
Neugebauer group
Max Planck Institute of Molecular Cell Biology and Genetics, Dresden
Pfotenhauerstrasse 108
01307 Dresden
Germany

e-mail: domi...@mpi-cbg.de
tel. +49 351 210 2481
The Unbearable Lightness of Molecular Biology

[Hiram Clawson]

Good Morning Ant�nio:

You are correct. Ensembl uses chromosome names of "1" where UCSC uses: "chr1"
You need to convert the Ensembl chromosome names to the UCSC names. The sed
command: sed -e 's/^\([0-9XY][0-9]*\)/chr\1/; s/^MT/chrM/;' converts names
in column one of a file from Ensembl to UCSC names.

--Hiram

Ant�nio Miguel de Jesus Domingues wrote:
> Hi Genomers,
>
> I am trying to convert wig.gz files (from QuEST chip-seq analysis) with the
> tool wigToBigWig. Initially the chromosome sizes were obtained with:
> fetchChromSizes hg19 > hg19.chrom.sizes
>
> But then I've ran into problems in the conversion to bigWig:
> wigToBigWig background_unnormalized.profile.wig.gz hg19.chrom.sizes
> background_unnormalized.profile.bw
>
> hashMustFindVal: '1' not found
> gzip: stdout: Broken pipe
> process exited with 1: "gzip -dc" in pipeline "gzip -dc"
>
> The only source of the problem that comes to my mind is that the reference
> genome for the the mapping and peak calling was from Ensembl, but this is a
> wild guess. Could you please help me with this?
>
> Cheers,

> Ant�nio