User: katherinedixon4

Reputation:
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New User
Location:
Canada
Last seen:
4 years, 3 months ago
Joined:
4 years, 4 months ago
Email:
k**************@gmail.com

Posts by katherinedixon4

<prev • 5 results • page 1 of 1 • next >
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Error in BETA basic in Cistrome
... Hi there, I am hoping to use the BETA tools in Cistrome to analyze RNA-seq data, however I haven't been able to complete the job without receiving an error. I have differential expression data from Cuffdiff and peak calls from MACS2 in bed format as input. I was wondering how I might be able to fix ...
beta cistrome written 4.3 years ago by katherinedixon410 • updated 4.3 years ago by fubar1.1k
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Comment: C: Intersect tool in Galaxy
... Thanks Jen! ...
written 4.3 years ago by katherinedixon410
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WIG file from MACS2
... Hi, I have been using MACS2 in Cistrome to call peaks from ChIP-seq data. It appears as though it's not possible to generate a wiggle file using MACS2, whereas there is an option to do so in MACS (within the Cistrome platform). I just wanted to make sure my understanding is correct? Thank you! ...
macs2 cistrome written 4.3 years ago by katherinedixon410 • updated 4.3 years ago by Bjoern Gruening5.1k
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Comment: C: Intersect tool in Galaxy
... Hi Jen, Thank you for your detailed answer! I have also been trying the new MACS2 on the Galaxy testing site, particularly to use the bdgbroadcall function that is available there. However I'm not sure what the last few columns in the output file represent, and haven't been able to find information ...
written 4.3 years ago by katherinedixon410
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Intersect tool in Galaxy
... Hi there, I am using the Intersect tool in Galaxy to find overlapping intervals of peak calls from ChIP-seq data. I haven't been able to determine what the values in the fifth column in the output interval file represent, and was hoping you could help? The values generally range from about 50-1000. ...
chip-seq galaxy written 4.3 years ago by katherinedixon410 • updated 4.3 years ago by Jennifer Hillman Jackson25k

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