Normalisation using Input DNA & calling peaks [Chip-seq]
Hello Biostars,
We all know that macs2 uses 'global background' for normalisation in 'mascs2 callpeaks' command. But is it possible that we can use our own BAM file (Input DNA) for normalisation ? I have Treatment, Wildtype & Input DNA BAMs. And how to call peaks if normalisation is done?
Please help. Thanks in advance!
1 answer
It is better that you have your own input sample. It is used as follows.
macs2 -t ChIP.bam -c Control.bam -f BAM -g hs -n test -B -q 0.01
where -t is Treatment or Wildtype and -c is input.
• 0 views
•
link
written
by
Satyajeet Khare
Log in to answer this question.
More posts like this
-
CUT&RUN spike in normalization in differential binding analysis (with replicates).
written by koleilat.karim •
-
How to make the Input track flat for ChIP-seq
written by dharitrisaikia162 •
-
Calculating area under the curve for broad peaks from ChIP-seq
written by mfeather •
-
Ori-Ter normalization [Chip-seq]
written by anu014
-
Narrow & Broad peaks from 'macs2 bdgdiff'
written by anu014
-
ChIP-seq analysis - More peaks in IP samples without activating the TF
written by avital1005 •
-
Difference in number of peaks called
written by anu014
-
Calling peaks with macs2 if not all replicates have a corresponding input-file
written by jklopp •
-
Extension size problem in MACS2
written by anu014
-
Macs2 And Peak Calling On Chromosome X
written by David
