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2.8k
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Can EPIC call peaks on files without control?
sicer epic ChIP-Seq peak-calling
updated 6.6 years ago by ▴ 980 • written 9.0 years ago by ▴ 270
0
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4
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3.4k
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Current status of EPIC peak caller
epic ChIP-Seq peak calling
updated 6.6 years ago by ▴ 980 • written 9.1 years ago by ▴ 270
0
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1
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2.6k
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Comment: C: Help defining contrasts in DESeq.
6.7 years ago by ariel.balter ▴ 270
1
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1
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2.6k
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Comment: C: Help defining contrasts in DESeq.
6.7 years ago by ariel.balter ▴ 270
3
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5
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2.6k
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Help defining contrasts in DESeq.
deseq contrasts r
6.7 years ago by ariel.balter ▴ 270
0
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2
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2.9k
views
Crazy log-likelihood values from MACS2 `bdgdiff`.
macs2 chipseq differential binding analysis
updated 7.1 years ago by • 0 • written 8.6 years ago by ▴ 270
3
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10
replies
3.6k
views
BWA or STAR for microbiome 16s multiple sequence alignment?
RNA-Seq alignment microbiome 16s
updated 7.1 years ago by 8.3k • written 7.1 years ago by ▴ 270
0
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0
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3.6k
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Comment: C: BWA or STAR for microbiome 16s multiple sequence alignment?
7.1 years ago by ariel.balter ▴ 270
0
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1
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3.6k
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Comment: C: BWA or STAR for microbiome 16s multiple sequence alignment?
7.1 years ago by ariel.balter ▴ 270
0
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0
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14k
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Answer: A: Is there any way to install RStudio (or any other powerful IDE for R) without ro
7.4 years ago by ariel.balter ▴ 270
14
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5
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15k
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6 follow
MACS2 with multiple replicates
ChIP-Seq MACS2
updated 7.5 years ago by ▴ 90 • written 8.6 years ago by ▴ 270
0
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0
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12k
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Comment: C: samtools view by chromosome region chr:1000-1001000 creates "unknown reference n
8.5 years ago by ariel.balter ▴ 270
0
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0
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14k
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Comment: C: What Is The Fastest Method To Determine The Number Of Positions In A Bam File Wi
8.5 years ago by ariel.balter ▴ 270
10
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2
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12k
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samtools view by chromosome region chr:1000-1001000 creates "unknown reference name" error
samtools
updated 8.5 years ago by 166k • written 8.5 years ago by ▴ 270
5
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1
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25k
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Comment: C: What is the definition of "read depth" vs "coverage"? (again...)
8.5 years ago by ariel.balter ▴ 270
14
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4
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25k
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What is the definition of "read depth" vs "coverage"? (again...)
coverage depth read depth
8.5 years ago by ariel.balter ▴ 270
3
votes
7
replies
5.4k
views
Forum: Typical costs for RNA-Seq analysis
RNA-Seq
updated 2.5 years ago by 45k • written 8.5 years ago by ▴ 270
0
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1
reply
5.4k
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Comment: C: Typical costs for RNA-Seq analysis
8.5 years ago by ariel.balter ▴ 270
0
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2
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5.4k
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Comment: C: Typical costs for RNA-Seq analysis
8.5 years ago by ariel.balter ▴ 270
0
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0
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15k
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Comment: C: MACS2 with multiple replicates
8.6 years ago by ariel.balter ▴ 270
0
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1
reply
26k
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Comment: Comment: Why use the qvalue package instead of p.adjust in R stats?
updated 3.6 years ago by 45k • written 8.6 years ago by ▴ 270
1
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0
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2.0k
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Comment: C: extracting several columns from a file
8.6 years ago by ariel.balter ▴ 270
0
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0
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15k
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Comment: C: MACS2 with multiple replicates
8.6 years ago by ariel.balter ▴ 270
0
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1
reply
11k
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Comment: C: What does "pileup" mean in the context of MACS2 peak caller?
8.6 years ago by ariel.balter ▴ 270
5
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3
replies
11k
views
What does "pileup" mean in the context of MACS2 peak caller?
ChIP-Seq pileup macs2
updated 8.6 years ago by 5.8k • written 8.6 years ago by ▴ 270
1
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1
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23k
views
Comment: C: Benchmark - Comparison of Different NGS Mappers
8.8 years ago by ariel.balter ▴ 270
1
vote
1
reply
7.6k
views
MACS2 Narrow peak (narrowPeak) output format
macs2 ChIP-Seq
updated 8.8 years ago by 20 • written 8.8 years ago by ▴ 270
0
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0
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6.8k
views
Answer: A: Why estimate fragment size of ChIP-seq with SPP when using Macs2 for peak callin
8.8 years ago by ariel.balter ▴ 270
0
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0
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5.5k
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Answer: A: sicer chip seq analysis
8.8 years ago by ariel.balter ▴ 270
0
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1
reply
7.4k
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Comment: C: Tophat and Bowtie installed with Conda not working on test data.
8.8 years ago by ariel.balter ▴ 270
0
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1
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7.4k
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Comment: C: Tophat and Bowtie installed with Conda not working on test data.
8.8 years ago by ariel.balter ▴ 270
0
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1
reply
2.6k
views
MACS2 coverage calculations
macs2 ChIP-Seq
8.8 years ago by ariel.balter ▴ 270
0
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2
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7.4k
views
Comment: C: Tophat and Bowtie installed with Conda not working on test data.
8.8 years ago by ariel.balter ▴ 270
1
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1
reply
7.4k
views
Comment: C: Tophat and Bowtie installed with Conda not working on test data.
8.8 years ago by ariel.balter ▴ 270
3
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10
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7.4k
views
Tophat and Bowtie installed with Conda not working on test data.
conda miniconda anaconda tophat bowtie
8.8 years ago by ariel.balter ▴ 270
0
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0
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3.8k
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Answer: A: bedtools multicov not running
8.9 years ago by ariel.balter ▴ 270
0
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0
replies
5.3k
views
Comment: C: Macs2 callpeak error: IndexError: list index out of range
8.9 years ago by ariel.balter ▴ 270
0
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1
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4.1k
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Comment: C: Chromosome sort order for bedops?
8.9 years ago by ariel.balter ▴ 270
5
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4
replies
4.1k
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Chromosome sort order for bedops?
bedops
updated 8.9 years ago by 36k • written 8.9 years ago by ▴ 270
3
votes
6
replies
2.5k
views
Trying to create short test bam not working.
samtools bam sam
updated 9.0 years ago by 14k • written 9.0 years ago by ▴ 270
9
votes
1
reply
11k
views
Difference between samtools DEPTH and MPILEUP
samtools mpileup depth ChIP-Seq reads
updated 9.1 years ago by 105k • written 9.1 years ago by ▴ 270
0
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1
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3.4k
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Comment: C: Current status of EPIC peak caller
9.1 years ago by ariel.balter ▴ 270
0
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0
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3.6k
views
Comment: C: MACS2 files not found even just after successfully installing
9.1 years ago by ariel.balter ▴ 270
0
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6
replies
3.1k
views
Chipseq sample or test data
ChIP-Seq
updated 9.1 years ago by 12k • written 9.1 years ago by ▴ 270
0
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0
replies
3.1k
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Comment: C: Chipseq sample or test data
9.1 years ago by ariel.balter ▴ 270
0
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1
reply
3.1k
views
Comment: C: Chipseq sample or test data
9.1 years ago by ariel.balter ▴ 270
0
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1
reply
3.6k
views
Comment: C: MACS2 files not found even just after successfully installing
9.1 years ago by ariel.balter ▴ 270
1
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4
replies
3.6k
views
MACS2 files not found even just after successfully installing
macs2 software error
updated 9.1 years ago by 105k • written 9.1 years ago by ▴ 270
0
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1
reply
2.6k
views
Comment: C: EPIC Error calculating readlength
9.1 years ago by ariel.balter ▴ 270
0
votes
3
replies
2.6k
views
EPIC Error calculating readlength
epic peak calling ChIP-Seq software error
9.1 years ago by ariel.balter ▴ 270
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