how to call weak peak using macs2
We are interesting in ChIP-seq small peak , we have avidence that the the small or weak peaks are functional sites , how to call weak peak using macs2？ I try to use the parameter q 0.05, but It can't call the weaker peaks.
• 1,291 views
•
link
written
by
huangweiping.official •
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
macs callpeak q value cutoff 1 and 0.05 with different peak result
written by miao •
-
Can I use All Peaks (MACS2 -q 1) for analysis?
written by Tian •
-
How to check wether Chip-seq worked or not
written by luckysardar171 •
-
Chip-seq peak calling best way usage of parameters
written by luckysardar171 •
-
Macs2: predicted fragment length less than 2*tag length
written by langya •
-
MACS2 gives negative estimated fragment length
written by dcheng1 •
-
[MACS2] False negative peak calling problem
written by dude.dude.law •
-
Macs2 failed for pooled samples
written by GR
-
peaks overlap: ATAC & CHIP seq
written by sophialovechan •
-
Macs2 And Peak Calling On Chromosome X
written by David
There is no gold standard answer for this. You will need a good input control, probably chromatin input is the best sequenced to similar depths as the IP samples. You can use dedicated replicate-aware peak callers such as
PePror use other filtering strategies that increase confidence in your calls such asIDRor custom strategies like "peak has to be in at least 2/3 samples at FDR below a certain threshold". Still, confidence in small peaks requires excellent data quality. If you have a poor antibody then you will have a hard time calling weak binding events. Are you after a transcription factor? How is data quality?