Hello,
We have ChIP-seq data that was from a single-end run with 35 bp reads. There are a few samples, with a different antibody used in each one. We aligned the reads and created autocorrelation plots (sometimes called cross-correlation) using HOMER and SPP. The DNA fragment length is around 150 bp, so we expect to see a single large peak at 150 bp.
Some of the samples look as we expect, but some have a large peak at 35 bp, and a small peak at 150 bp. Does this mean that something is wrong with these samples?
Thanks!
We have ChIP-seq data that was from a single-end run with 35 bp reads. There are a few samples, with a different antibody used in each one. We aligned the reads and created autocorrelation plots (sometimes called cross-correlation) using HOMER and SPP. The DNA fragment length is around 150 bp, so we expect to see a single large peak at 150 bp.
Some of the samples look as we expect, but some have a large peak at 35 bp, and a small peak at 150 bp. Does this mean that something is wrong with these samples?
Thanks!
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