I have a TF ChIP-seq time course study with read length of 125bp Paired end around 30 to 50M paired reads in different libraries. Analysis pipeline in short: Map to mm10 with Bowtie2, remove duplicates using samtools, peak calling by MACS2 using BAM files as input (with format as BAMPE). The number of peaks I get is in two digits. But when I shut down the dynamic lambda (--nolambda option) the peak numbers reaches 4-5 digits. I look at those peaks in genome browser and I see really beautiful peaks in ChIP sample and no peak in input control. I fail to understand why MACS2 calls those peaks only when the --nolambda option is used. I have used various other parameters of MACS as well but I fail to get the peak numbers high until unless I use --nolambda option.
I've tried other options of MACS as well but nothing is working out for me. Could this be the possibility that larger read length and paired end data is not something that MACS could handle?
Any advice/suggestion is most welcome and appreciated