How get density plot TSS region for genes of interest

Question

[BISEP]

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

Answer 1

[jared.andrews07]

deepTools plotProfile tool does what you want.

[BISEP]

@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

[jared.andrews07]

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.

[BISEP]

@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

[jared.andrews07]

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

[BISEP]

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

[QX]

Hi jared.andrews07 , which bed file shall I used, bed file for the gene (from gtf) or the bed file generated from the macs2 peak calling?

[jared.andrews07]

Depends on your question. Are you interested in the signal profile at peaks or at genic regions?

Post your own question if it's more involved than this, piggybacking on old questions is generally discouraged as it makes relevant questions and answers harder to find for people.

[QX]

thank for your answer and suggestion