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Question: Bam file can not convert into bigwig
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gravatar for liya.huo
4.0 years ago by
liya.huo • 0
United States
liya.huo • 0 wrote:

Hello,

I got a bam file and upload to the Galaxy.  When I convert it into bigwig, it gives me that message:1 is not found in chromosome sizes file.

Is there somebody can help me with that?

Thank you in advance.
galaxy • 1.3k views
ADD COMMENT • link •
modified 4.0 years ago by Daniel Blankenberg ♦♦ 1.7k • written 4.0 years ago by liya.huo • 0
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gravatar for Daniel Blankenberg
4.0 years ago by
Daniel Blankenberg ♦♦ 1.7k
United States
Daniel Blankenberg ♦♦ 1.7k wrote:

Sounds like a mismatch between between chromosome names, where your bam has e.g. "1", but the dbkey/genome build uses "chr1".
ADD COMMENT • link written 4.0 years ago by Daniel Blankenberg ♦♦ 1.7k

Dear Daniel,

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,

RSH

ADD REPLY • link written 3.5 years ago by rahel14350 • 0
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