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Question: Bedgraph column 1
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gravatar for jlocker
20 months ago by
jlocker • 0
United States
jlocker • 0 wrote:

I used Bedtools to generate Bedgraphs from Bam files. Column 1 only contains a number that is not preceded by chr. How do I fix this.
galaxy • 443 views
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modified 20 months ago by Jennifer Hillman Jackson ♦ 25k • written 20 months ago by jlocker • 0
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gravatar for Jennifer Hillman Jackson
20 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

There are tools in the group Text Manipulation that can be used to add on a "chr" to the chromosome names. However, this will not always make the file match up with a UCSC-sourced reference genome without other changes. So if you decide to do this, be sure to double check the chromosome names before using the data with other tools or before attempting to visualize the data in the UCSC Browser.

Mapping against the correct target genome is a better way to fix the mismatch problem (map against the UCSC-sourced genome instead of the Ensembl-sourced genome). Using the same exact reference genome for all steps in an analysis ensures that data mismatch errors (or incomplete results) do not come up.

Thanks! Jen, Galaxy team
ADD COMMENT • link written 20 months ago by Jennifer Hillman Jackson ♦ 25k
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