how to proceed with ChIP seq analysis

[AmitPande]

Hi,

I am new to ChIP seq analysis and would like to understand a few things. I want to analyze histone modification through SICER and already have the 36 base pair result aligned to the human genome.
Since the genomic co-ordinates always overlap e.g.,
chr1 0 36 ATCGCGCGAACTCGCGCGCGCTCGTCGTCAA 1000 +
chr1 36 52 ATAGGGtCTCACATCTCGCGcTCGTCTCGCGAA 1000 +

so on should I merge these intervals against the reference genome before running it against the resting cell ip through SICER to determine enrichment or run the intervals just like the way they are....

kindly guide me....

warm regards,
Amit

[ETHANol]

I'm not really sure what you are getting at. Work flow goes as:
1) Align reads to reference genome (perhaps this was done for you). You should have two files, your input and ChIPed sample.
2) Convert file (ELAND, SAM, BAM or whatever you have) to a BED file.
3) Run SICER as described in readme.txt

On a side note, I'll be glad to instruct you in person in you fly me down to Mauritious. Ha ha. Any open positions?

[AmitPande]

dataset is kept here ....so I dont know the ChIped sample file that you are talking about

http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE26320

and I am trying to learn ...I would appreciate if you could explain more it would be kind on your part....

warm regards,
.....