Question: Convert BAM into bigwig for chicken
0
gravatar for d92b41001
3.9 years ago by
d92b410010
United States
d92b410010 wrote:

Hi,

I used functions of “Create a BedGraph of genome coverage” and “Wig/BedGraph-to-bigWig” in Galaxy to convert a BAM file into a bigwig file. It worked well when BAM files were aligned onto a chicken galGal4 reference genome downloaded from the UCSC Genome Browser. However, it doesn’t work when the chicken reference genome were downloaded from Ensembl (Release 72 or 75). The below is the error message from “Wig/BedGraph-to-bigWig”. Could you help me? Thanks a lot.

error

An error occurred with this dataset:

hashMustFindVal: '1' not found

Error running wigToBigWig.

Gary

bigwig bam • 2.1k views
ADD COMMENTlink modified 3.8 years ago by Jennifer Hillman Jackson25k • written 3.9 years ago by d92b410010
1
gravatar for Jennifer Hillman Jackson
3.8 years ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

You must use the same reference genome for all steps in an analysis. Even the chromosome identifiers must be an exact match. If you want to compare sequences to different assemblies, then you need to map the data to each.

More about reference genomes and mismatch issues is explained here:
https://galaxyproject.org/support/chrom-identifiers/

(link updated 3-2018)

Best, Jen, Galaxy team

ADD COMMENTlink modified 5 months ago • written 3.8 years ago by Jennifer Hillman Jackson25k

I have a question regarding the IGV and bigwig conversion that maybe you can help me.
I am trying to convert a .bam file to bigwig with mouse genome (mm10) to visualize the reads and I am getting this error:

hashMustFindVal: 'GL456210.1' not found

and this is my command:

wigToBigWig  -clip mm10.chrom.sizes ./control1.bw

I already found out that I need to convert the chromosome Ids to UCSC. I want to know is this common to convert the IDs from ENSEMBLE to UCSC for bigwig conversion? Do you have any idea about it?

Many thanks in advance,

ADD REPLYlink written 3.2 years ago by rahel143500
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