How get density plot TSS region for genes of interest
1
0
Entering edit mode
6 weeks ago
BISEP • 0

Hello I have chipseq data wanted do TSS region and gene body density plot from list of genes can any one suggest me how can I do this

Thank you

Chipseq • 330 views
ADD COMMENT
0
Entering edit mode
6 weeks ago

deepTools plotProfile tool does what you want.

ADD COMMENT
0
Entering edit mode

@jared.andrews07 Thanks for response, I was trying to use plotprofile i am little bit confused usage of the command. I have genes list of genes lets say 50 for this genes I want density plot for tss region is it possible do this in plotprofile

Thank you

ADD REPLY
0
Entering edit mode

Yes, see the usage example on that page. You'll have to run computeMatrix with a bed file containing each of your genes along with bigwigs for your signal.

ADD REPLY
0
Entering edit mode

@jared.andrews07 Can I convert GTF file to bed file, and get the genes what I wanted and run the computeMatrix, TSS region okay, What about genebody? how I have to specify the parameter

ADD REPLY
0
Entering edit mode

Have you tried following the examples? Please read the computeMatrix docs closely - you can use a GTF directly.

ADD REPLY
0
Entering edit mode

Yes I have read the computematrix file, for gene body I got little bit confused

ADD REPLY

Login before adding your answer.

Traffic: 2648 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6