No called peaks from macse 2 and the alignment rate 90%

Question

[sahhomaha]

Hi I am facing a problem in analysing my chip seq data. I ran the bowtie 2 to generate aligment read SAM, then I used the samtools view, sort,rm to generate cleam bam file ready for pack calling. The aligment rate was 90% , 80% in some of my data. But the peack called was 100-800/ and in one case0. I do not know if my chip seq failled and I must reapeat the experiment or there is a technical issue.

[Ming Tommy Tang]

load the bam file or bigwig (make it from bam) to IGV, and visually check if there any enrichment in the genome or not. if not, the experiment failed most likely.

[Prakash]

There could be possibly two issue I can see here ..either there is very low sequencing depth, if not then there is ChIP efficiency problem.. also did you use input sample for peak calling?