Question: Error of wig/BedGraph-to-bigWig converter
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gravatar for d92b41001
2.7 years ago by
d92b410010
United States
d92b410010 wrote:

Hi,

I have a ChIP-Seq BAM file aligned on the chicken galGal3 reference genome using Bowtie2. I used “Create a BedGraph of genome coverage” under BEDTools to convert it into a bedgraph file. After that, the file was converted into a bigwig file using “Wig/BedGraph-to-bigWig converter” under “Convert Formats” (bigwig_fig1). However, it showed an error: hashMustFindVal: '1' not found (bigwig_fig1). The BAM file can be uploaded onto UCSC Genome Browser (bigwig_fig2). However, when the bedgraph was uploaded onto the UCSC Genome Browser, there is an error as below:

Unrecognized format line 1 of https://usegalaxy.org/root/display_as?id=19919161&display_app=ucsc&authz_method=display_at:1 0 67 0 (note: chrom names are case sensitive, e.g.: correct: 'chr1', incorrect: 'Chr1', incorrect: '1')

Sorry, couldn't locate 1:0-806 in genome database

At the same time, the BAM file processed by the same method can be successfully converted into a bigwig file and uploaded onto UCSC Genome Browser.

Could you help me? Thank you very much.

Gary

bigwig_fig1

bigwig_fig2

bigwig_fig3

bedbraph ucsc galaxy bigwig bam • 1.1k views
ADD COMMENTlink modified 2.7 years ago by Bjoern Gruening4.8k • written 2.7 years ago by d92b410010
0
gravatar for Bjoern Gruening
2.7 years ago by
Bjoern Gruening4.8k
Germany
Bjoern Gruening4.8k wrote:

Hi,

my guess is that you are mixing different annotation sources. Please make sure the chromosome naming is in every file and every reference genome identical. For example UCSC names chromosomes like this chr1 others simply name it 1.

Hope this helps,

Bjoern
 

ADD COMMENTlink written 2.7 years ago by Bjoern Gruening4.8k
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