Hi all,
It's my first attempt at ChIP-seq. I optimized fixation time, shearing, IP. I confirmed my ChIP was working by qPCR. Prepped libraries and sequenced on a HiSeq 1500 (SE, 50 cycles to start just to make sure library prep gives me results I expect).
I analyzed the resulting data as follows:
1. map reads using bowtie (identical sequences not yet collapse, working on it!)
2. convert to bam format
3. plot profiles using ngsplot
I got some unexcepted results for my input, which look very similar to my ChIP samples. The major problem is that I am getting a peak at TSS and smaller peak at TES. I was expecting the input profile to be flat.
Is this a common problem? Do I have contamination in my library prep?
Here are my profiles of input and PAF1 ChIP (transcription elongation factor responsible for H3K4me3).
Thanks in advance for any wisdom you have to share.
It's my first attempt at ChIP-seq. I optimized fixation time, shearing, IP. I confirmed my ChIP was working by qPCR. Prepped libraries and sequenced on a HiSeq 1500 (SE, 50 cycles to start just to make sure library prep gives me results I expect).
I analyzed the resulting data as follows:
1. map reads using bowtie (identical sequences not yet collapse, working on it!)
2. convert to bam format
3. plot profiles using ngsplot
I got some unexcepted results for my input, which look very similar to my ChIP samples. The major problem is that I am getting a peak at TSS and smaller peak at TES. I was expecting the input profile to be flat.
Is this a common problem? Do I have contamination in my library prep?
Here are my profiles of input and PAF1 ChIP (transcription elongation factor responsible for H3K4me3).
Thanks in advance for any wisdom you have to share.
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