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