Changing the content of the BED file columns to be recognized by genome browser

Question: Changing the content of the BED file columns to be recognized by genome browser

6 months ago by

Ath.T • 20

Ath.T • 20 wrote:

Hello

I am doing RNA-seq analysis using usegalaxy.com 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 )

QNAME  FLAG  RNAME   POS  MAPQ  CIGAR
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

Thanks

rna-seq microbial ucsc bed • 239 views

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modified 6 months ago by Jennifer Hillman Jackson ♦ 25k • written 6 months ago by Ath.T • 20

6 months ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Your data is correctly formatted for BED except for the header line. The BED format specification is described here: https://galaxyproject.org/learn/datatypes/#bed

This genome as loaded at the UCSC Microbial browser (http://microbes.ucsc.edu/) 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:

The primary chromosome is named just "chr" at UCSC. How to make the change to the first column is covered in this FAQ https://galaxyproject.org/support/chrom-identifiers/.
Change as needed the database attribute for the dataset to be assigned to "streCoel". This does not change the file/dataset content, but rather describes the dataset as a whole. FAQ https://galaxyproject.org/support/metadata/.
Optionally add a track line using Graph/Display Data > Build custom track for UCSC genome browser. If you are not sure what these are, check the help here: http://genome.ucsc.edu/goldenPath/help/customTrack.html.
Once all is done, use the link inside the final BED dataset: display at UCSC archaea.

Here is a test history of your data to model after https://usegalaxy.org/u/jen/h/test-history-ucsc-microbial-browser

Thanks, Jen, Galaxy team

ADD COMMENT • link written 6 months ago by Jennifer Hillman Jackson ♦ 25k

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