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2.2k
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Can EPIC call peaks on files without control?
sicer epic ChIP-Seq peak-calling
updated 5.0 years ago by ▴ 960 • written 7.4 years ago by ▴ 260
0
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4
replies
2.6k
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Current status of EPIC peak caller
epic ChIP-Seq peak calling
updated 5.0 years ago by ▴ 960 • written 7.5 years ago by ▴ 260
0
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1
reply
1.9k
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Comment: C: Help defining contrasts in DESeq.
5.2 years ago by ariel.balter ▴ 260
1
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1
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1.9k
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Comment: C: Help defining contrasts in DESeq.
5.2 years ago by ariel.balter ▴ 260
3
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5
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1.9k
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Help defining contrasts in DESeq.
deseq contrasts r
5.2 years ago by ariel.balter ▴ 260
0
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2
replies
2.3k
views
Crazy log-likelihood values from MACS2 `bdgdiff`.
macs2 chipseq differential binding analysis
updated 5.5 years ago by • 0 • written 7.0 years ago by ▴ 260
3
votes
10
replies
2.5k
views
BWA or STAR for microbiome 16s multiple sequence alignment?
RNA-Seq alignment microbiome 16s
updated 5.5 years ago by 8.2k • written 5.5 years ago by ▴ 260
0
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0
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2.5k
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Comment: C: BWA or STAR for microbiome 16s multiple sequence alignment?
5.5 years ago by ariel.balter ▴ 260
0
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1
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2.5k
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Comment: C: BWA or STAR for microbiome 16s multiple sequence alignment?
5.5 years ago by ariel.balter ▴ 260
0
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0
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11k
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Answer: A: Is there any way to install RStudio (or any other powerful IDE for R) without ro
5.8 years ago by ariel.balter ▴ 260
13
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5
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12k
views
6 follow
MACS2 with multiple replicates
ChIP-Seq MACS2
updated 5.9 years ago by ▴ 90 • written 7.0 years ago by ▴ 260
0
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0
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11k
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Comment: C: samtools view by chromosome region chr:1000-1001000 creates "unknown reference n
7.0 years ago by ariel.balter ▴ 260
0
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0
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12k
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Comment: C: What Is The Fastest Method To Determine The Number Of Positions In A Bam File Wi
7.0 years ago by ariel.balter ▴ 260
10
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2
replies
11k
views
samtools view by chromosome region chr:1000-1001000 creates "unknown reference name" error
samtools
updated 7.0 years ago by 161k • written 7.0 years ago by ▴ 260
5
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1
reply
23k
views
Comment: C: What is the definition of "read depth" vs "coverage"? (again...)
7.0 years ago by ariel.balter ▴ 260
13
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4
replies
23k
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What is the definition of "read depth" vs "coverage"? (again...)
coverage depth read depth
7.0 years ago by ariel.balter ▴ 260
3
votes
7
replies
4.6k
views
Forum: Typical costs for RNA-Seq analysis
RNA-Seq
updated 11 months ago by 43k • written 7.0 years ago by ▴ 260
0
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1
reply
4.6k
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Comment: C: Typical costs for RNA-Seq analysis
7.0 years ago by ariel.balter ▴ 260
0
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2
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4.6k
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Comment: C: Typical costs for RNA-Seq analysis
7.0 years ago by ariel.balter ▴ 260
0
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0
replies
12k
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Comment: C: MACS2 with multiple replicates
7.0 years ago by ariel.balter ▴ 260
0
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1
reply
23k
views
Comment: Comment: Why use the qvalue package instead of p.adjust in R stats?
updated 2.0 years ago by 43k • written 7.0 years ago by ▴ 260
1
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0
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1.4k
views
Comment: C: extracting several columns from a file
7.0 years ago by ariel.balter ▴ 260
0
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0
replies
12k
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Comment: C: MACS2 with multiple replicates
7.0 years ago by ariel.balter ▴ 260
0
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1
reply
9.0k
views
Comment: C: What does "pileup" mean in the context of MACS2 peak caller?
7.1 years ago by ariel.balter ▴ 260
5
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3
replies
9.0k
views
What does "pileup" mean in the context of MACS2 peak caller?
ChIP-Seq pileup macs2
updated 7.1 years ago by 5.7k • written 7.1 years ago by ▴ 260
1
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1
reply
19k
views
Comment: C: Benchmark - Comparison of Different NGS Mappers
7.2 years ago by ariel.balter ▴ 260
1
vote
1
reply
7.0k
views
MACS2 Narrow peak (narrowPeak) output format
macs2 ChIP-Seq
updated 7.2 years ago by 20 • written 7.3 years ago by ▴ 260
0
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0
replies
5.7k
views
Answer: A: Why estimate fragment size of ChIP-seq with SPP when using Macs2 for peak callin
7.2 years ago by ariel.balter ▴ 260
0
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0
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4.9k
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Answer: A: sicer chip seq analysis
7.2 years ago by ariel.balter ▴ 260
0
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1
reply
6.3k
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Comment: C: Tophat and Bowtie installed with Conda not working on test data.
7.3 years ago by ariel.balter ▴ 260
0
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1
reply
6.3k
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Comment: C: Tophat and Bowtie installed with Conda not working on test data.
7.3 years ago by ariel.balter ▴ 260
0
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1
reply
2.1k
views
MACS2 coverage calculations
macs2 ChIP-Seq
7.3 years ago by ariel.balter ▴ 260
0
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2
replies
6.3k
views
Comment: C: Tophat and Bowtie installed with Conda not working on test data.
7.3 years ago by ariel.balter ▴ 260
1
vote
1
reply
6.3k
views
Comment: C: Tophat and Bowtie installed with Conda not working on test data.
7.3 years ago by ariel.balter ▴ 260
3
votes
10
replies
6.3k
views
Tophat and Bowtie installed with Conda not working on test data.
conda miniconda anaconda tophat bowtie
7.3 years ago by ariel.balter ▴ 260
0
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0
replies
3.0k
views
Answer: A: bedtools multicov not running
7.3 years ago by ariel.balter ▴ 260
0
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0
replies
4.4k
views
Comment: C: Macs2 callpeak error: IndexError: list index out of range
7.4 years ago by ariel.balter ▴ 260
0
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1
reply
3.1k
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Comment: C: Chromosome sort order for bedops?
7.4 years ago by ariel.balter ▴ 260
5
votes
4
replies
3.1k
views
Chromosome sort order for bedops?
bedops
updated 7.4 years ago by 35k • written 7.4 years ago by ▴ 260
3
votes
6
replies
1.8k
views
Trying to create short test bam not working.
samtools bam sam
updated 7.4 years ago by 14k • written 7.4 years ago by ▴ 260
9
votes
1
reply
10.0k
views
Difference between samtools DEPTH and MPILEUP
samtools mpileup depth ChIP-Seq reads
updated 7.5 years ago by 104k • written 7.5 years ago by ▴ 260
0
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1
reply
2.6k
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Comment: C: Current status of EPIC peak caller
7.5 years ago by ariel.balter ▴ 260
0
votes
0
replies
2.9k
views
Comment: C: MACS2 files not found even just after successfully installing
7.5 years ago by ariel.balter ▴ 260
0
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6
replies
2.2k
views
Chipseq sample or test data
ChIP-Seq
updated 7.5 years ago by 12k • written 7.5 years ago by ▴ 260
0
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0
replies
2.2k
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Comment: C: Chipseq sample or test data
7.5 years ago by ariel.balter ▴ 260
0
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1
reply
2.2k
views
Comment: C: Chipseq sample or test data
7.5 years ago by ariel.balter ▴ 260
0
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1
reply
2.9k
views
Comment: C: MACS2 files not found even just after successfully installing
7.5 years ago by ariel.balter ▴ 260
1
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4
replies
2.9k
views
MACS2 files not found even just after successfully installing
macs2 software error
updated 7.5 years ago by 104k • written 7.5 years ago by ▴ 260
0
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1
reply
2.1k
views
Comment: C: EPIC Error calculating readlength
7.6 years ago by ariel.balter ▴ 260
0
votes
3
replies
2.1k
views
EPIC Error calculating readlength
epic peak calling ChIP-Seq software error
7.6 years ago by ariel.balter ▴ 260
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