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15
votes
1
answer
847
views
1
answer
error while reading bigwig files in computeMatrix (deeptools)
deeptools bigwig coverage computematrix written 14 months ago by Lila M • 810 • updated 5 days ago by Biostar ♦♦ 20
3
votes
0
answers
148
views
0
answers
Visualize top 10 increasing peaks of the ATAC-seq data
deeptools atac-seq heatmap written 9 days ago by kinalimeric • 20
2
votes
1
answer
102
views
1
answer
bamCompare output values ChIP/input normalization
deeptools chip-seq bamcompare normalization written 13 days ago by marco • 0 • updated 12 days ago by colin.kern • 900
2
votes
1
answer
121
views
1
answer
Chip-Seq input normalization with deeptools
deeptools chip-seq written 14 days ago by srhic • 0 • updated 14 days ago by jared.andrews07 ♦ 5.3k
0
votes
1
answer
676
views
1
answer
deepTools white dots on black background
deeptools written 3.0 years ago by Kasthuri • 260 • updated 16 days ago by Biostar ♦♦ 20
10
votes
2
answers
137
views
2
answers
Normalization of ATAC SEQ data for the proper deeptools heatmap
deeptools atac seq normalization written 18 days ago by kinalimeric • 20 • updated 18 days ago by ATpoint ♦ 31k
2
votes
1
answer
76
views
1
answer
deeptools plotProfile plots inconsistently
plotprofile deeptools plotheatmap written 4 weeks ago by Ekalavya • 10 • updated 4 weeks ago by colin.kern • 900
0
votes
2
answers
103
views
2
answers
Removing outliers from bigwig files
deeptools next-gen chip-seq written 5 weeks ago by srhic • 0
0
votes
0
answers
79
views
0
answers
Deeptools Normalization Problem
deeptools chip-seq written 5 weeks ago by silvia.raineri • 0
10
votes
0
answers
192
views
0
answers
ATAC-seq data and deepTools: Small detail with impact on output
atacseq deeptools readlength bigwig forum written 6 weeks ago by gable_works • 40 • updated 6 weeks ago by ATpoint ♦ 31k
3
votes
1
answer
91
views
1
answer
Normalize BigWig's for # of reads in peaks and sequencing depth
atacseq deeptools written 8 weeks ago by Zeel • 0 • updated 8 weeks ago by ATpoint ♦ 31k
3
votes
2
answers
150
views
2
answers
deepTools/Galaxy Optimize K-Means Clusters - Elbow Plot
deeptools galaxy chip-seq sequencing written 3 months ago by Ready2Rapture • 20 • updated 12 weeks ago by Mensur Dlakic • 4.0k
113
votes
9
answers
28k
views
72 follow
9
answers
Forum: Visualization of ChIP-seq data using Heatmaps (Updated: 06/10/16)
homer deeptools forum chip-seq ngsplot visualization written 4.1 years ago by Sinji • 3.0k • updated 3 months ago by Ömer An • 200
3
votes
2
answers
216
views
6 follow
2
answers
Plot read density across a normalized gene model for its each exon/intron length
deeptools next-gen chip-seq R python written 3 months ago by kashiff007 • 130 • updated 3 months ago by benformatics • 1.5k
1
vote
1
answer
2.3k
views
1
answer
Deeptools error - Solving environment: failed with initial frozen solve
deeptools atac-seq python error written 5 months ago by dydy_cristina • 0 • updated 5 months ago by yztxwd • 300
2
votes
1
answer
372
views
1
answer
computeMatrix bed format files
deeptools chip-seq written 5 months ago by Morris_Chair • 170
2
votes
0
answers
179
views
0
answers
Is there a way to get multiBigwigSummary with 1-based coordinates instead of 0-based?
deeptools multibigwigsummary written 6 months ago by Zee_S • 50
0
votes
0
answers
132
views
0
answers
Representing several BAM files into one?
deeptools bam bamcompare written 6 months ago by raquelgarza95 • 50
4
votes
2
answers
1.1k
views
6 follow
2
answers
[ChIP-seq. signal plot] How to align the based line of different samples?
deeptools chip-seq normalization written 2.2 years ago by chiefcat • 140 • updated 6 months ago by ricardo3889 • 20
1
vote
1
answer
294
views
1
answer
Plotting chip signal at TSSs with deeptools
deeptools chip-seq computematrix written 7 months ago by srhic • 0 • updated 7 months ago by Devon Ryan ♦ 94k
2
votes
1
answer
289
views
1
answer
Draw coverage plot from bed file
deeptools coverage bed file written 7 months ago by ben.kunfang • 10 • updated 7 months ago by Alex Reynolds ♦ 29k
2
votes
0
answers
1.3k
views
0
answers
plotProfile with mean of bigwig files
plotprofile deeptools average bigwig mean written 2.7 years ago by ildem • 50 • updated 8 months ago by Biostar ♦♦ 20
1
vote
2
answers
3.6k
views
2
answers
Overlapping regions in a BedGraph file
gro-seq bedgraph chip-seq deeptools written 4.2 years ago by Sam • 90 • updated 10 months ago by Simply Bioinformatics • 170
5
votes
2
answers
421
views
6 follow
2
answers
.sra to bam conversion results in a "< myfile > does not have BAM or CRAM format error"
sra-toolkit samtools deeptools written 10 months ago by jordi.planells • 100 • updated 10 months ago by genomax ♦ 80k
5
votes
1
answer
473
views
1
answer
Issue running deeptools on cluster via snakemake
deeptools snakemake written 10 months ago by camerond • 150 • updated 10 months ago by russhh ♦ 5.2k
1
vote
1
answer
721
views
1
answer
Deeptools for ChIP-Seq
deeptools chip-seq heatmap written 11 months ago by yugen30 • 10
2
votes
1
answer
1.3k
views
1
answer
show the names of the genes on the Y axis on the heatmap Deeptools
deeptools chip-seq rna-seq written 3.5 years ago by Bioiris • 0 • updated 10 months ago by yugen30 • 10
0
votes
1
answer
588
views
1
answer
Chip Seq analysis for H3K27me3,H3K27ac and K4me1 enrichment
deeptools chip-seq written 11 months ago by Researcher • 50 • updated 11 months ago by jared.andrews07 ♦ 5.3k
0
votes
1
answer
288
views
1
answer
bamCompare the result if 0
deeptools chip-seq bamcompare written 12 months ago by HI • 0 • updated 12 months ago by Devon Ryan ♦ 94k
8
votes
1
answer
469
views
1
answer
How extract the longest overlap?
bedtools deeptools bedops intersect overlap written 12 months ago by star • 230 • updated 12 months ago by Biostar ♦♦ 20
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