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Question: Phastcons score under hi-seq peaks
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gravatar for mdp07vm
9 months ago by
mdp07vm • 20
United States
mdp07vm • 20 wrote:

Hi, I would like to get the phastcons score (vertebrate first then mammals) under Chip-seq peaks and ATAC-seq peaks genome wide via Galaxy (or other technique). What's the best and simplest way to accomplish this?

Thanks!

Victor
ucsc annotation phastcons chip-seq • 319 views
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modified 9 months ago by Jennifer Hillman Jackson ♦ 25k • written 9 months ago by mdp07vm • 20
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gravatar for Jennifer Hillman Jackson
9 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

To get all of the data (covering the entire genome), Phastcons data can be extracted from the Get Data > UCSC Table browser tool for smaller datasets. If larger (these will probably be large), go to the UCSC downloads area http://genome.ucsc.edu and obtain the files directly then upload them to Galaxy for analysis (using FTP). Help for understanding UCSC data content and querying table browser are at the UCSC site plus they host a Google group for Q&A.

To directly obtain UCSC track data based on a set of genomic intervals (peaks), the tool Operate on Genomic Intervals > Profile Annotations for a set of genomic intervals can be used.

Galaxy support FAQs: https://galaxyproject.org/support/

Thanks! Jen, Galaxy team
ADD COMMENT • link modified 9 months ago • written 9 months ago by Jennifer Hillman Jackson ♦ 25k
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