Hello I am doing ChIP-Seq analysis I have two sets some list of genes for this I wanted coverage information TSS and genebody can anybody suggest me how can do that. is there any R related tools any method available please mention
Thank you
There are a lot of different methods to do that, but I can recommend deeptools, especially the computeMatrix tool combined with the plotProfile tool. It is easy to use, with quite a lot of flexibility, and also a very good documentation.
@Carlo Yague
Thanks for the reply I have already tried deeptools as u said different method are available can you suggest me
You can also use bedtools genomecov in the command line to generate the matrix then load it in R and process as needed. Also there is the ChIPseekR R package.
@Carlo Yague Thank for the suggestions do you know in deeptools which bedformat we have to use in the computeMatrix genewise or transcript wise because when I am providing GTF instade of bed its giving me gene number if I gave the transcript containing bed file its not showing gene number so I was confused and wanted clarify so try new options. documentation genewise bedfile is mentioned deeptools doc
Can please help me with a example of bed file
What do you mean gene number ? can you show a few lines of your gtf file, bed file, and deeptools output ?
GTF file
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