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
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
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