bedGraph -----> saving as a table in the other format

Question

[olekw1115]

Dear all,

I had the data with ChIP-Seq Peaks in bedGraph format. I can open it with IGV.

But I would like to get the results of ChIP-Seq as the table (for example in excel, etc.) - I only need the list of genes from my bedGraph document with the information, if there was a peak for this gene or no. (I'm very sorry, I'm new here and I don't know how should I call it professionally, but that's what I would like to get from my bedGraph document)

Is there such possibility to get such data from bedgraph?

Best wishes

[Manvendra Singh]

bedGraph is like a bed file, so do you have gene names too where bedGraph file has co-ordinates?

e.g.

chromA  chromStartA  chromEndA  dataValueA
  chromB  chromStartB  chromEndB  dataValueB

do you have an extra coloumn with gene names?

if not then

can you also work on linux terminal ?

Then I can tell you, Its easy.

[olekw1115]

I have got only gene names. There is unfortunately no extra column.

I'm not working on linux terminal.

Thanks!

Answer 1

[Ming Tommy Tang]

Hi, you need a bed peak file (http://genome.ucsc.edu/FAQ/FAQformat.html#format1) which is generated by peak calling software like MACS http://liulab.dfci.harvard.edu/MACS/

then, you can annotate the peaks by other packages such as ChIPpeakAnno http://www.bioconductor.org/packages/release/bioc/html/ChIPpeakAnno.html

ChIPseeker http://www.bioconductor.org/packages/2.14/bioc/html/ChIPseeker.html

or web GUI http://manticore.niehs.nih.gov:8080/pavis/

http://cru.genomics.iit.it/AnnotateGenomicRegions/index.jsf

[olekw1115]

Thank you! I will try it

[olekw1115]

Hi, I have a problem in opening MACS. I have read that I can use Python to open it, so I have tried it, but it does't work. Does anybody know how could I open it?

(I'm very sorry for such a simple question, but I was looking for an answer in the Internet and trying different things, but it doesn't help)

Thank you:)