I'm in need of some help in order to move forward:
I'm a grad student in a lab brand new to next-gen sequencing, I'm trying to run ChIPseq experiments with ER alpha Ab (sc543) on an ER+ breast cancer cell line, and I've now tried to analyze two sequencing runs on two samples, with the analysis workflow summarized below.
My question: could over-amplification during library preparation cause the peaks in my ChIP sample to be attenuated, or is it more likely that my antibody just didn't enrich specific genomic regions? Both input and ChIP samples were amplified 18 cycles.
Illumina Hi-Scan > bowtie2 > SortSam > macs14 (ChIP and Input) > ~1100 peaks with FDR range of 75-100
.wig files for treat and control generated by MACS have almost identical profiles for any given chromosome when viewed with IGV.
I'm a grad student in a lab brand new to next-gen sequencing, I'm trying to run ChIPseq experiments with ER alpha Ab (sc543) on an ER+ breast cancer cell line, and I've now tried to analyze two sequencing runs on two samples, with the analysis workflow summarized below.
My question: could over-amplification during library preparation cause the peaks in my ChIP sample to be attenuated, or is it more likely that my antibody just didn't enrich specific genomic regions? Both input and ChIP samples were amplified 18 cycles.
Illumina Hi-Scan > bowtie2 > SortSam > macs14 (ChIP and Input) > ~1100 peaks with FDR range of 75-100
.wig files for treat and control generated by MACS have almost identical profiles for any given chromosome when viewed with IGV.
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