User: mdp07vm

gravatar for mdp07vm
mdp07vm20
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Status:
New User
Location:
United States
Last seen:
3 months, 3 weeks ago
Joined:
2 years, 8 months ago
Email:
m******@gmail.com

Posts by mdp07vm

<prev • 10 results • page 1 of 1 • next >
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Comment: C: Intersect the intervals of two datasets (Galaxy Version 1.0.0)
... Excellent. Thanks Jen. Victor ...
written 3 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 3 months ago by mdp07vm20 • updated 3 months ago by Jennifer Hillman Jackson22k
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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 4 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 4 months ago by mdp07vm20 • updated 4 months ago by Martin Čech ♦♦ 4.0k
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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 14 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 14 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 14 months ago by mdp07vm20 • updated 14 months ago by Jennifer Hillman Jackson22k
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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 2.7 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 2.7 years ago by mdp07vm20
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HOMER motif search, conservation and correlate ChIP-seq to RNA-seq
... Hi there, I need help or advice in the following questions which may not be related to each other but are all important for the analyses that I'm currently working on. I'm analyzing my ATAC-seq and ChIP-seq data as well as correlating them to my RNA-seq data.  1) When I use HOMER (annotatePeaks.pl ...
chip-seq rna-seq written 2.7 years ago by mdp07vm20

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Popular Question 2.7 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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