Question: Difference in number of peaks called
0
gravatar for anu014
2.2 years ago by
anu014170
India
anu014170 wrote:

Hi Biostars,

I have used macs2 for calling peaks in chip-seq data. Firstly, I called peaks for antibiotic-treated sample & wild-type sample individually. After I ran macs2 with antibiotic-treated sample as treatment group (-t) & wild-type sample as control group (-c). Lastly, I ran the tool using antibiotic-treated sample as control group (-c) & wild-type sample as treatment group (-t). I got following number of peaks:

Antibiotic-treated S :  1007
WT S: 100
Antibiotic-treated vs WT : 46
WT vs Antibiotic-treated : 90

I am not getting the stats. If 100 were picked up individually & 90 peaks are called in WT vs Antibiotic treated run, then in Antibiotic-treated vs WT , the remaining 10 peaks should be checked against peaks present in Antibiotic-treated group. Why am I getting 46 peaks?

command parameters: # Command line: callpeak -f BAMPE -g 6748384 -B --mfold 1 60 --broad --broad-cutoff 0.1 --bw 300 --buffer-size 100000 --qvalue 0.05 --slocal 1000 --llocal 10000 --cutoff-analysis --fe-cutoff 1.0

Thank you in advance! :)

peakcalling chip-seq macs2 • 949 views
ADD COMMENTlink modified 17 months ago by colindaven1.7k • written 2.2 years ago by anu014170
0
gravatar for colindaven
17 months ago by
colindaven1.7k
Hannover Medical School
colindaven1.7k wrote:

Shouldn't you be calling each against the Input (same chip-seq process, but not applying the antibody) for these data, not against WT or control ? Have you looked at the plotfingerprints method from Deeptools - in Galaxy ?

ADD COMMENTlink written 17 months ago by colindaven1.7k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 890 users visited in the last hour