Question: Changing the content of the BED file columns to be recognized by genome browser
gravatar for Ath.T
6 months ago by
Ath.T20 wrote:


I am doing RNA-seq analysis using and this is my first time to do that. I have a problem in the bed file, UCSC genome browser does not recognize the file, as it does not contain ''chr1'' in the QNAME column. The BED file that I`ve created as the following: (The format of the gene reference is FASTA )

AL939114.1  0  139  J00125:34:HTJT7BBXX:5:1101:16670:2703/2  8  +

How can I change the content of QNAME to chr1 and How can I insert start and end in the position column instead of '' J00125:34:HTJT7BBXX:5:1101:16670:2703/2'' ??.

Any suggestions


rna-seq microbial ucsc bed • 239 views
ADD COMMENTlink modified 6 months ago by Jennifer Hillman Jackson25k • written 6 months ago by Ath.T20
gravatar for Jennifer Hillman Jackson
6 months ago by
United States
Jennifer Hillman Jackson25k wrote:


Your data is correctly formatted for BED except for the header line. The BED format specification is described here:

This genome as loaded at the UCSC Microbial browser ( has the source and chromosome/plasmid identifiers described at that web server. Search by "Streptomyces coelicolor" to review the details and make sure that you mapped against the same build/version. UCSC often modifies the accessions to a standardized format, but if the original source is the same, the genomes are a match.

Then modify:

Here is a test history of your data to model after

Thanks, Jen, Galaxy team

ADD COMMENTlink written 6 months ago by Jennifer Hillman Jackson25k
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