How should I begin with the chip-seq data analysis for a non model organism (no reference organism available)? Also if someone could suggest good reading material on the same.
I think you can not work without at least a genome that is being sequenced. There is a technic called ChIA-PET that allows to perform ChIPseq analysis without a fully annotated genome: it has been developed by a group on Singapour . Here is one of the reference:
Genome Biol. 2010;11(2):R22. doi: 10.1186/gb-2010-11-2-r22. Epub 2010 Feb 25.
ChIA-PET tool for comprehensive chromatin interaction analysis with paired-end tag sequencing.
Li G, Fullwood MJ, Xu H, Mulawadi FH, Velkov S, Vega V, Ariyaratne PN, Mohamed YB, Ooi HS, Tennakoon C, Wei CL, Ruan Y, Sung WK.
http://www.ncbi.nlm.nih.gov/pubmed/20181287
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