I am new to the CHIP-seq analysis. I am basically trying to call peaks using MACS 2 with the proccessed data of mitochondrial DNA only in bedgraph format given in the accession number GSE48176 under the link https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE48176. I used three treated samples and three control samples in the analysis, with the command
macs2 callpeak \
-f BED \
-g hs \
--mfold 2 30 \
--nomodel \
-t GSM1171656_Hela-TFAM-12228.36mers.v0.chrM.wig.sorted.bed \
GSM1171657_Hela-TFAM-12277.36mers.v0.chrM.wig.sorted.bed \
GSM1171658_Hela-TFAM-12526.36mers.v0.chrM.wig.sorted.bed \
GSM1171659_Hela-TFAM-PrepK-12332.36mers.v0.chrM.wig.sorted.bed \
-c GSM1171652_Hela-Input-12229.36mers.v0.chrM.wig.sorted.bed \
GSM1171653_Hela-Input-12278.36mers.v0.chrM.wig.sorted.bed \
GSM1171654_Hela-Input-12527.36mers.v0.chrM.wig.sorted.bed \
GSM1171655_Hela-Input-PrepK-12333.36mers.v0.chrM.wig.sorted.bed \
-n TFAM-12228.36mers.v0chrM
I should have many peaks as Circos plot given in the paper "Genome-Wide Analysis Reveals Coating of the Mitochondrial Genome by TFAM".But All I got from MACS2 callpeak output was only 1 200bp fragment long peak. Nothing other than that.
My argument is same as given in the paper except I used --no model as without this argument I got an error.
Attached figure is the output I got from MACS2 in the excel format along with the circos plot from the paper I got the CHIP-seq bedgraph file from.
Can someone please describe What I did wrong in my chip-seq analysis...? Bugs me a great deal
This image on the left is the circos plot shown in the literature and is also the data that I want to obtain peak values for. and On the right is the excel sheet of the MACS2 callpeak result with only one peak given as output.
