Q: ChIPSeq calling peaks with SPMR

[bioinfograd]

Hello, I am running the command below

macs2 callpeak -t 18.chip.sorted.bam
-c 12.input.sorted.bam
-f BAMPE -g hs --broad-cutoff 0.1 -B --SPMR -n His_Rep2
--outdir /SPMR/eachind

I understand that when using SPMR I can use this to visualize signal tracks and should not use it for calling peaks from the bedgraphs subsequently generated but can I use the peaks bed/xls file that is generated after running the above command? I think that is fine?

[bioinfograd]

I guess a follow up is if using the file is fine why would you use bgdiff and not just look at the peaks being called? Why do the added step? Does it just call better peaks?

[taoliu]

@bioinfograd Thanks for asking! Yes. You can use the peaks bed/xls generated from callpeak --SPMR since the option --SPMR only affects the bedGraph output.

Regarding your follow-up question on bdgdiff, the differential peak calling is not simply a peak-overlapping process. Same as differential gene expression analysis, a gene is regarded as 'expressed' in both conditions -- i.e. above certain FPKM cutoff in both conditions, doesn't mean it is not differentially expressed.