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Question: Filtering list of regions to known refseq areas
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gravatar for juanjoven2
4.3 years ago by
juanjoven2 • 0
United States
juanjoven2 • 0 wrote:

Hi, I have a set of Chip-seq-like data aligned to mm9, and have run SICER to peak call, thus generating a list of possible hits.  I would like to limit these peak call to known gene regions (introns/exons), and avoid looking at intergenic regions.  Can someone point out the best way of approaching this filtering process?

Many thanks in advance,
galaxy chip-seq • 942 views
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modified 4.3 years ago by Jennifer Hillman Jackson ♦ 25k • written 4.3 years ago by juanjoven2 • 0
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gravatar for Jennifer Hillman Jackson
4.3 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Extracting the "Known Genes" or "RefSeq Genes" from UCSC (RefSeq genes are included in Known genes) in BED6 format is the first step (per exon/intron/etc - you can choose the regions to include on the forms). Assign as an interval dataset along with your peak results in an interval format and try the tools in the group "Operate on Genomic Intervals". BEDTools also has coordinate comparison tools, so you can try others, but I would start with the first.

Best, Jen, Galaxy team
ADD COMMENT • link written 4.3 years ago by Jennifer Hillman Jackson ♦ 25k
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