how to peak caling the abnormal chipseq bam files against the input

Question

[zhangyan4963]

Since our chipseq results had a problem, our unique aligned reads of the chipseq is 30% of the Input reads. but we need to do peak calling of the chipseq. in the seq-company, they got a bad results that nearly contain no peaks. I guess they didn't normalized the input file.

So how can I do this peak calling? Macs or Sicer is better ? Any parameter or Pre-Processing can solve this problems?

[gauravsingh.singh86]

You can try with galaxy-server.

Answer 1

[Ian]

I would recommend MACS2 with defaults (appropriate to your genome) as there is a linear normalisation of reads between the two samples, effectively bringing down the more numerous sample to the lower sample. Another important consideration is the genome you are dealing with and the number of reads that MACS will finally use (non-redundant reads). For a human/mouse transcription factor the general advice is 20 million, but sometimes you can get away with less depending on the binding profile.