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4
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1
answer
97
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1
answer
MACS2 option for ATAC seq?
peak-calling macs2 chip-seq atac-seq dnase-seq written 1 day ago by star • 100
0
votes
0
answers
228
views
0
answers
ATAC-seq transcription factor binding prediction
transcription factor atac-seq rna-seq written 3 months ago by Lucy • 0 • updated 3 days ago by am2622 • 0
0
votes
0
answers
135
views
0
answers
Job: Bioinformatics and Biostatistics Analysts & Research Scientists in Systems Immunology, Allen Inst for Immunology
next-gen atac-seq R job facs rna-seq written 5 days ago by hbolouri • 0
0
votes
1
answer
67
views
1
answer
Differential Binding in Partek
partek chip-seq atac-seq written 9 days ago by DVA • 490 • updated 9 days ago by kgosche • 0
7
votes
1
answer
129
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1
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Duplicated ATAC-Seq peaks called by MACS2
macs peak calling macs2 atac-seq written 16 days ago by Gary • 450 • updated 16 days ago by geek_y ♦ 9.1k
1
vote
1
answer
70
views
1
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Merging peak files for unionized set
bedtools next-gen atac-seq written 17 days ago by aam458 • 0 • updated 16 days ago by trausch • 1.2k
0
votes
0
answers
123
views
0
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How to compare footprints (motifs found) from two different packages after peak calling using MACS2?
chip-seq atac-seq written 23 days ago by vatsal.mehra • 0
1
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0
answers
97
views
0
answers
Homer annotatePeaks.pl custom GTF
gtf homer atac-seq written 23 days ago by Lucy • 0
0
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0
answers
136
views
0
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Iterative trimming using bowtie
bowtie2 iterative trimming alignment atac-seq written 24 days ago by ancient_learner • 610
0
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0
answers
126
views
0
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Aligning RNA-seq and ATAC-seq gene annotations
homer gene annotation atac-seq rna-seq written 5 weeks ago by Lucy • 0
1
vote
2
answers
239
views
2
answers
comparing ATAC-seq/ChIP-seq peaks
chip-seq atac-seq written 5 weeks ago by sckinta • 480 • updated 5 weeks ago by ATpoint ♦ 13k
3
votes
0
answers
217
views
0
answers
Finding motifs with Homer for obscure species.
genome homer atac-seq written 3 months ago by a.rex • 170 • updated 6 weeks ago by Biostar ♦♦ 20
5
votes
0
answers
407
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6 follow
0
answers
Explaining fragment distribution plots from ATAC-seq
atac-seq written 3 months ago by a.rex • 170 • updated 7 weeks ago by Biostar ♦♦ 20
0
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0
answers
157
views
0
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CENTIPEDE - values from fitCentipede
R atac-seq centipede written 3 months ago by Lucy • 0 • updated 8 weeks ago by Biostar ♦♦ 20
2
votes
1
answer
228
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1
answer
Bigwig format and operation
bigwig chip-seq atac-seq written 8 weeks ago by oriolebaltimore • 60
3
votes
2
answers
503
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6 follow
2
answers
ATACseqQC - Cut-site probability greater than 1?
atac-seq atacseqqc written 11 months ago by ldyer2006 • 30 • updated 10 weeks ago by Lizzy • 0
2
votes
1
answer
304
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1
answer
High PCR duplication rate in ATAC-seq library
sequencing next-gen atac-seq pcr duplicate written 11 weeks ago by ttsutsui1028 • 20 • updated 11 weeks ago by ATpoint ♦ 13k
0
votes
0
answers
245
views
0
answers
Explaining PCA plots made from BigWig coverage files in DeepTools
deeptools atac-seq written 12 weeks ago by a.rex • 170 • updated 12 weeks ago by RamRS ♦ 20k
0
votes
0
answers
189
views
0
answers
Is it common for ATAC-peaks to be located in Repeat Masker annotated regions?
genome atac-seq written 3 months ago by a.rex • 170
2
votes
2
answers
285
views
2
answers
Seemingly contradictory ATAC-seq conclusions from a Science journal paper?
atac-seq written 3 months ago by solo7773 • 70 • updated 3 months ago by ATpoint ♦ 13k
0
votes
0
answers
231
views
0
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Integrative analysis of omics studies using machine learning
chip-seq atac-seq rna-seq machine learning written 3 months ago by Firas • 0
0
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0
answers
251
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0
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Fseq versus MACS2 for ATAC-seq
atac-seq written 3 months ago by a.rex • 170
6
votes
1
answer
411
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5 follow
1
answer
Using featureCounts and DESeq2 to look at differences between ATAC-seq conditions.
R next-gen atac-seq written 3 months ago by a.rex • 170 • updated 3 months ago by ATpoint ♦ 13k
3
votes
1
answer
406
views
1
answer
Acceptable duplication levels in ATAC-Seq data
sequencing atac-seq pcr duplicates written 4 months ago by bowwow • 0 • updated 4 months ago by Devon Ryan ♦ 88k
1
vote
1
answer
357
views
1
answer
Finding differences in motif enrichment between ATAC peak samples?
homer atac-seq written 4 months ago by a.rex • 170 • updated 4 months ago by James Ashmore • 2.6k
3
votes
1
answer
210
views
1
answer
Correlating putative enhancer elements with gene expression
enhancer gene expression atac-seq rna-seq written 4 months ago by rbronste • 230 • updated 4 months ago by kristoffer.vittingseerup • 1.4k
3
votes
3
answers
393
views
3
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How can I find motifs under individual ATAC-peaks?
atac-seq written 4 months ago by a.rex • 170 • updated 4 months ago by jared.andrews07 • 1.8k
0
votes
0
answers
312
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0
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problem with HOMER findMotifsGenome.pl
homer atac-seq written 4 months ago by ste.lu • 40
4
votes
1
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618
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5 follow
1
answer
Can be merged biological replicates?
chip-seq macs2 peak-calling atac-seq rna-seq written 5 months ago by star • 100 • updated 4 months ago by ZZzzzzhong • 190
0
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0
answers
227
views
0
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featureCounts allowMultiOverlap - fractional or not?
featurecounts atac-seq written 4 months ago by Lucy • 0
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