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
deepTools plotProfile tool does what you want.
@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
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.
@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
Have you tried following the examples? Please read the computeMatrix docs closely - you can use a GTF directly.
Yes I have read the computematrix file, for gene body I got little bit confused
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