Forum: (Closed) Multiple Intersect in ChIPseq analysis
0
gravatar for georgess.dan
8 months ago by
georgess.dan40
georgess.dan40 wrote:

Hello, I have some ChIPseq data but I do not know how to write/use code so I am trying to build a workflow on UseGalaxy.org to analyze Treatment-vs-Control in 3 biological replicates sequenced on Illumina. Based on some of the online forums, I need to "intersect" (and not "merge") the data between 3 biological replicates.

1) On pipeline design: - Do I need to fist run the intersct of 3 dataset (e.g. 3 treatments, 3 control), then run the output of 3 treatment against the output of 3 controls on MACS. - or, do I need to first run MACS on Treatment vs Control for each biological replicate, then run intersect on the output files.

2) On the use of the Multiple Intersect function (under BEDTools) in building a Workflow: How to I compare 2 or 3 files if the total allowed input is 1 BED file and 1 genome file? Am I misunderstanding what the purpose of the tool is?

Any expert opinion would be greatly appreciated! Dan

ADD COMMENTlink modified 5 months ago by linying91140 • written 8 months ago by georgess.dan40

Hello georgess.dan!

Questions similar to yours can already be found at:

We have closed your question to allow us to keep similar content in the same thread.

If you disagree with this please tell us why in a reply below. We'll be happy to talk about it.

Cheers!

ADD REPLYlink written 5 months ago by Jennifer Hillman Jackson23k
Please log in to add an answer.
The thread is closed. No new answers may be added.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 85 users visited in the last hour