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Old 08-24-2018, 10:46 AM   #1
ewersj
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Post Determining quality of ChIP-seq data

Hi all,

I am brand new to ChIP-seq, and I'm doing some practice data analysis. I'm trying to determine whether any trimming or post processing is necessary before mapping the reads. Can anyone help me to interpret the following assays, and make this determination? It's quite possible that I'm not even looking in the right place, so any help would be appreciated.

For example, sample GS-7:





I am asking because the Galaxy Chip-seq tutorial assumes data of high quality, and I cannot necessarily make the same assumption.

Thank you!

Jeff
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Old 08-27-2018, 05:24 AM   #2
kmcarr
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Jeff,

Always pre-process read data before downstream analysis. This includes adapter trimming and quality filtering even if you don't expect to find much if any adapter.

As an aside you should perform an additional AmpureXP (or equivalent) clean up on these libraries before sequencing; many contain adapter dimer contamination (the small peak ~130bp). This is especially important if you plan to sequence them on a HiSeq 4000. Even a very small contamination of adapter dimer may produce a significant number of useless reads.
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