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Old 01-13-2014, 05:46 PM   #1
muhe1985
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Location: New Orleans

Join Date: Jan 2014
Posts: 4
Smile Newbie's Question on align published Chip-Seq data

I think these question are so green I feel even embarrassed to ask:

What I want to do is to align the binding peaks of the transcription factors I am working with to a genome locus I am interested in (as a mean to find the potential mechanism for how the the transcription factor I am interested in regulates the locus containing multiple other genes.)

For this purpose, I was looking for an introduction like 1, which analyzing software should I start with for this kind of simple purpose? I am wondering around Galaxy and IGV or CisGenome, I want to start with the one with the most user base, and of course, more friendly to wetbiologist who spend most of time on bench work.

2, I attached the Begining part of the GFF/BED file I am working on, I want to output a peaks track profile with the locus I am interested in as reference gene, ideally, I want to be flexible when I need to add peak file of other transcription factors to compare the potential overlapping of binding peaks. at the end, I want to extract the sequence fasta file (so I could focusing on some of the peaks and repeat the experiment by Chip-qPCR).

The above sounds like a really newbie stuff,can some one recommend a introductory post or even text book for me that I could do this part professionally?




The GFF file I am working with has the information as showed below

Seqname Source Feature Start End Score Strand Frame Group
chr1 Sole_search_nkxelanda05fdr001p5 TagPeak 3284430 3284669 18 + . chr1_3284430_3284669
chr1 Sole_search_nkxelanda05fdr001p5 TagPeak 3357210 3357419 19 + . chr1_3357210_3357419
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