Question: Phastcons score under hi-seq peaks
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gravatar for mdp07vm
6 months ago by
mdp07vm20
United States
mdp07vm20 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

ADD COMMENTlink modified 6 months ago by Jennifer Hillman Jackson25k • written 6 months ago by mdp07vm20
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gravatar for Jennifer Hillman Jackson
6 months ago by
United States
Jennifer Hillman Jackson25k 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 COMMENTlink modified 6 months ago • written 6 months ago by Jennifer Hillman Jackson25k
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