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5
votes
1
answer
111
views
1
answer
MACS2 option for ATAC seq?
peak-calling macs2 chip-seq atac-seq dnase-seq written 3 days ago by star • 110
7
votes
1
answer
180
views
1
answer
ChipSeq using MACS2 - option to not call peaks with only few reads ?
macs2 chip-seq written 16 days ago by Bastien Hervé ♦ 3.3k
5
votes
1
answer
83
views
1
answer
shall we consider -- keep-dup all when we removed duplication?
duplicate macs2 peak-calling chip-seq written 4 days ago by star • 110 • updated 4 days ago by benformatics • 490
0
votes
1
answer
100
views
1
answer
Normalizing ChIP-seq and ATAC-seq data?
normalization macs2 chip-seq alignment written 6 days ago by star • 110
3
votes
2
answers
906
views
2
answers
Narrow & Broad peaks from 'macs2 bdgdiff'
macs2 next-gen chip-seq peakcalling sequencing written 17 months ago by anu014 • 160 • updated 16 days ago by MMa • 250
7
votes
1
answer
133
views
1
answer
Duplicated ATAC-Seq peaks called by MACS2
macs peak calling macs2 atac-seq written 19 days ago by Gary • 450 • updated 18 days ago by geek_y ♦ 9.1k
1
vote
1
answer
158
views
1
answer
ChIP-Seq Analysis allele specific way?
vcf chip-seq ngs macs2 ase written 27 days ago by Susmita Mandal • 20 • updated 26 days ago by Devon Ryan ♦ 88k
4
votes
2
answers
225
views
2
answers
ChIP-Seq experiment, MACS2 bdgpeakcall 0 fold-change, pvalue and qvalue
macs2 chip-seq written 8 weeks ago by Bastien Hervé ♦ 3.3k
1
vote
1
answer
664
views
1
answer
Problem with MACS2 results
ngs macs2 written 9 months ago by eilluecaf • 0 • updated 3 months ago by Biostar ♦♦ 20
0
votes
0
answers
322
views
0
answers
Macs2: predicted fragment length less than 2*tag length
macs2 chip-seq tagsize written 5 months ago by langya • 30 • updated 3 months ago by Biostar ♦♦ 20
7
votes
3
answers
341
views
7 follow
3
answers
macs2 conda installation problem
software error osx macs2 python version written 3 months ago by jcs92 • 0 • updated 3 months ago by h.mon ♦ 23k
1
vote
0
answers
284
views
0
answers
MACS2 --SPMR and --nolambda usage for version 2.1.2
macs2 chip-seq written 3 months ago by varunorama • 0
0
votes
1
answer
669
views
1
answer
Crazy log-likelihood values from MACS2 `bdgdiff`.
chipseq macs2 differential binding analysis written 22 months ago by ariel.balter • 130 • updated 3 months ago by yinyeya • 0
4
votes
1
answer
618
views
5 follow
1
answer
Can be merged biological replicates?
chip-seq macs2 peak-calling atac-seq rna-seq written 5 months ago by star • 110 • updated 4 months ago by ZZzzzzhong • 190
0
votes
0
answers
225
views
0
answers
When using MACS2 with -f BAM, it is possible to have a shift other than 0?
macs macs2 written 5 months ago by Lucy • 0 • updated 4 months ago by Biostar ♦♦ 20
1
vote
1
answer
278
views
1
answer
Determine peak summits after IDR analysis
peak summits macs2 idr written 5 months ago by Lucy • 0 • updated 5 months ago by Alex Reynolds ♦ 27k
3
votes
1
answer
264
views
1
answer
MACS2: Albeit outdir definition, my output goes to folder of input
macs2 chip-seq written 5 months ago by gdeniz • 0
0
votes
1
answer
330
views
1
answer
shift direction in ATAC/DNase data?
macs2 chip-seq atac-seq dnase-seq written 5 months ago by star • 110
0
votes
1
answer
358
views
1
answer
Inconsistency between number of reads in Samtools flagstat and Macs2 total tags.
macs2 peak calling atac chip-seq written 6 months ago by ahmadammarmalik • 0 • updated 6 months ago by genomax ♦ 62k
0
votes
0
answers
204
views
0
answers
Meaning of mfold upper limit?
mfold macs2 chip-seq written 6 months ago by mbk0asis • 410
1
vote
0
answers
272
views
0
answers
What parameter values to change in peak calling with MACS2 when calculating IDR afterwards?
macs2 idr chip-seq written 6 months ago by salamandra • 180
0
votes
1
answer
633
views
1
answer
file "_peaks.bed" on macs2
macs2 chip-seq peakcall written 20 months ago by Brice222 • 30 • updated 7 months ago by Biostar ♦♦ 20
6
votes
2
answers
848
views
5 follow
2
answers
How can I look at find 'open chromatin' from ATAC-seq data using MACS2
macs2 atac-seq written 7 months ago by a.rex • 170 • updated 7 months ago by ATpoint ♦ 13k
1
vote
1
answer
279
views
1
answer
how i get get same length of peaks by macs2
macs2 chip-seq written 7 months ago by mikysyc2016 • 30
3
votes
2
answers
1.8k
views
7 follow
2
answers
ATAC-seq: differential peaks using macs2 bdgdiff yields strange results
macs2 atac-seq written 12 months ago by stephenz • 10 • updated 7 months ago by Alternative • 220
2
votes
4
answers
2.2k
views
4
answers
Empty output from MACS2 when using control
peak calling macs2 chip-seq written 3.1 years ago by lm687 • 50 • updated 7 months ago by oriolebaltimore • 60
0
votes
1
answer
460
views
1
answer
Doubt using HOMER annotatePeaks.pl
homer macs2 chip-seq written 8 months ago by nanoide • 10 • updated 8 months ago by b.nota ♦ 6.0k
8
votes
2
answers
768
views
8 follow
2
answers
Peak calling using macs2?
macs2 chip-seq peaks peak-calling written 8 months ago by star • 110 • updated 8 months ago by RamRS ♦ 20k
1
vote
3
answers
2.4k
views
5 follow
3
answers
MACS2 with multiple replicates
macs2 chip-seq written 22 months ago by ariel.balter • 130 • updated 8 months ago by Hmd • 10
0
votes
3
answers
767
views
3
answers
MACS2 output (fold enrichment)
macs chipseq macs2 written 8 months ago by samantha_jeschonek • 50 • updated 8 months ago by roma • 120
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