User: mdp07vm

gravatar for mdp07vm
mdp07vm20
Reputation:
20
Status:
New User
Location:
United States
Last seen:
3 months, 3 weeks ago
Joined:
3 years, 5 months ago
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m******@gmail.com

Posts by mdp07vm

<prev • 11 results • page 1 of 2 • next >
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Phastcons score under hi-seq peaks
... 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 ...
chip-seq phastcons annotation ucsc written 3 months ago by mdp07vm20 • updated 3 months ago by Jennifer Hillman Jackson25k
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Comment: C: Intersect the intervals of two datasets (Galaxy Version 1.0.0)
... Excellent. Thanks Jen. Victor ...
written 12 months ago by mdp07vm20
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Intersect the intervals of two datasets (Galaxy Version 1.0.0)
... Hi, I intersected two of my datasets using the 'Intersect the intervals of two datasets (Galaxy Version 1.0.0)' tool. It provided a an output of the intersected intervals but there wasn't any description to the columns (i.e. what they represent) in the tool webpage. Does anyone know what the last 4 ...
chip-seq alignment written 12 months ago by mdp07vm20 • updated 12 months ago by Jennifer Hillman Jackson25k
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Comment: C: Error downloading Galaxy
... I'm running on mac osx 10.7.5. I will check the answer out. Thanks! ...
written 13 months ago by mdp07vm20
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Error downloading Galaxy
... Hi, I'm trying to download Galaxy in order to import a tool from the repository. I followed all the steps in the following page: https://galaxyproject.org/admin/get-galaxy/ but came across the following error message after running the command $ sh run.sh . ``` ImportError: dlopen(/Users/epsteinlab/ ...
galaxy software error written 13 months ago by mdp07vm20 • updated 13 months ago by Martin Čech ♦♦ 4.7k
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Comment: C: Excluding promoter and exon peaks
... I think I just found out how to do this. I will let you know if I encounter any problems. Thanks. ...
written 23 months ago by mdp07vm20
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Comment: C: Excluding promoter and exon peaks
... Hi Jen, Thanks for the suggestions. I'm working with mm9 hosted by UCSC. I tried the Get Data>UCSC Main method, but I'm struggling to find the track (or tracks) that represents promoters/exons. It will be terrific if you can point me to the correct track/s. Appreciate your help in this! Thanks, ...
written 23 months ago by mdp07vm20
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Excluding promoter and exon peaks
... Hi, would appreciate if someone could advise me on how to exclude promoter and exon peaks after peak calling. I've performed a TF chip-seq and did the peak calling using HOMER. For the next part of my analysis, I wish to focus only on intergenic and intronic regions for data intersection study with ...
chip-seq written 23 months ago by mdp07vm20 • updated 23 months ago by Jennifer Hillman Jackson25k
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Comment: C: HOMER motif search, conservation and correlate ChIP-seq to RNA-seq
... Thanks Jennifer for the link. I'm a Biostar user but I wasn't aware that HOMER is available - hence, my use of HOMER on my own system. Are you able to advice on the rest of the questions i.e. 2 and 3? Thanks, Victor ...
written 3.4 years ago by mdp07vm20
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Answer: A: HOMER motif search, conservation and correlate ChIP-seq to RNA-seq
... Hi Jen, no i'm not using this tool on Galaxy. I'm using it on my computer. Is there a tool (or tools) on Galaxy that can help accomplish my workflow above? Thanks. ...
written 3.4 years ago by mdp07vm20

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Popular Question 3.4 years ago, created a question with more than 1,000 views. For HOMER motif search, conservation and correlate ChIP-seq to RNA-seq

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