MACS2 peaks filtering
I have created a merged_BAM file by merging 100 individual bam files.
I am calling chip-seq peaks on merged_BAM file using MACS2
I want to obtain p-value threshold to filter out the MACS2 peaks
One of the ways I am doing is using IDR on 3 copies of merged_BAM that are created by randomly subsampling 33% of the original merged_BAM file.
merged_BAM_replicate 1( 33% of original merged_BAM) merged_BAM_replicate 2( 33% of original merged_BAM) merged_BAM_replicate 3( 33% of original merged_BAM)
Do you have other suggestions?
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Fixed peak width in ENCODE TFs ChIP-seq
written by DavideBrex •
-
ChIP seq peak annotation
written by tsomakiank •
-
CUT&Tag data processing: peak caller choice and typical peak size profile
written by nihilior •
-
Understanding Chip-seq data (ENCODE and other resources)
written by r.kalampaliki •
-
How to get the pooled-replicate narrowPeak file for IDR peak-list
written by ben.kunfang •
-
Does IDR (irreproducible discovery rate) higher mean less 'reproducible' or vice versa?
written by sckinta
-
Chip-seq on pooled replicates
written by GR
-
Macs2 failed for pooled samples
written by GR
-
How can I increase the number of peaks using macs2 peak caller?
written by GK1610
-
Irreproducible Discovery Rate
written by Dataminer
Why do you want to filter out peaks? MACS has internal q-value cutoffs, is there anything wrong with it? By subsampling, you reduce statistical power. Please explain what your goal is.