Almost no peak output after peakcalling of mtDNA with MACS2

Almost no peak output after peakcalling of mtDNA with MACS2

0

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 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

enter image description hereThis 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.


bioinformatics


MACS2


chip-seq


mtDNA


python

• 20 views

Read more here: Source link