Question: Filtering list of regions to known refseq areas
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gravatar for juanjoven2
3.7 years ago by
juanjoven20
United States
juanjoven20 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 • 812 views
ADD COMMENTlink modified 3.7 years ago by Jennifer Hillman Jackson25k • written 3.7 years ago by juanjoven20
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gravatar for Jennifer Hillman Jackson
3.7 years ago by
United States
Jennifer Hillman Jackson25k 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 COMMENTlink written 3.7 years ago by Jennifer Hillman Jackson25k
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