How to get the coverage information in chip seq for TSS and genebody

Question

[luckysardar171]

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

Answer 1

[Carlo Yague]

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.

[luckysardar171]

@Carlo Yague

Thanks for the reply I have already tried deeptools as u said different method are available can you suggest me

[Carlo Yague]

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.

[luckysardar171]

@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

[Carlo Yague]

What do you mean gene number ? can you show a few lines of your gtf file, bed file, and deeptools output ?

[luckysardar171]

GTF file
when I am using this gtf file getting error so I converted into bed using gtf2bed I am sharing link which has bedfile and deeptools output bed and output