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2
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2
replies
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Trimmomatic: How to improve FastQC report by adjusting the thresholds in running Trimmomatic?
RNA-Seq Trimmomatic FastQC
updated 2.9 years ago by ▴ 10 • written 6.0 years ago by ▴ 70
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1
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3.4k
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Comment: C: RNA-seq long reads vs. transcripts
4.5 years ago by tunl ▴ 70
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0
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3.4k
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Comment: C: RNA-seq long reads vs. transcripts
4.5 years ago by tunl ▴ 70
0
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1
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3.4k
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Comment: C: RNA-seq long reads vs. transcripts
4.5 years ago by tunl ▴ 70
6
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7
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3.4k
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RNA-seq long reads vs. transcripts
RNA-Seq long reads assembly
4.5 years ago by tunl ▴ 70
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1
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1.2k
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Comment: C: A question about differential expression analysis
4.8 years ago by tunl ▴ 70
3
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5
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1.2k
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A question about differential expression analysis
RNA-Seq single-cell RNA-seq DE analysis
updated 4.8 years ago by 102k • written 4.8 years ago by ▴ 70
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0
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2.9k
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Comment: C: Differential expression analysis tool for single cell RNA-seq data
4.8 years ago by tunl ▴ 70
0
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0
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2.9k
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Comment: C: Differential expression analysis tool for single cell RNA-seq data
4.8 years ago by tunl ▴ 70
3
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4
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2.9k
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Differential expression analysis tool for single cell RNA-seq data
single-cell RNA-seq DE analysis RNA-Seq
updated 4.8 years ago by ★ 1.2k • written 4.8 years ago by ▴ 70
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0
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1.2k
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Comment: C: Length distribution of PacBio RNA-seq
4.9 years ago by tunl ▴ 70
4
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7
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1.2k
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Length distribution of PacBio RNA-seq
RNA-Seq PacBio long reads
4.9 years ago by tunl ▴ 70
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1
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1.2k
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Comment: C: Length distribution of PacBio RNA-seq
4.9 years ago by tunl ▴ 70
0
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0
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1.2k
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Comment: C: Length distribution of PacBio RNA-seq
4.9 years ago by tunl ▴ 70
0
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0
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1.5k
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Comment: C: Question about downloading RNA-seq long reads and short reads for the same sampl
4.9 years ago by tunl ▴ 70
0
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0
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1.5k
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Comment: C: Question about downloading RNA-seq long reads and short reads for the same sampl
4.9 years ago by tunl ▴ 70
0
votes
0
replies
1.5k
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Comment: C: Question about downloading RNA-seq long reads and short reads for the same sampl
4.9 years ago by tunl ▴ 70
0
votes
1
reply
1.5k
views
Comment: C: Question about downloading RNA-seq long reads and short reads for the same sampl
4.9 years ago by tunl ▴ 70
0
votes
0
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1.5k
views
Comment: C: Question about downloading RNA-seq long reads and short reads for the same sampl
4.9 years ago by tunl ▴ 70
5
votes
10
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1.5k
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Question about downloading RNA-seq long reads and short reads for the same sample
RNA-Seq long reads PacBio
updated 4.9 years ago by ▴ 70 • written 4.9 years ago by ▴ 70
0
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1
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1.5k
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Comment: C: Question about downloading RNA-seq long reads and short reads for the same sampl
4.9 years ago by tunl ▴ 70
4
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7
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2.0k
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What determines which tests are performed in Cuffdiff? Only two types of tests were performed in our Cuffdiff run
RNA-Seq Cuffdiff
updated 4.9 years ago by 20 • written 6.0 years ago by ▴ 70
0
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1
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3.1k
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Comment: C: Question about some features in Cytoscape.js (or D3.js)
5.5 years ago by tunl ▴ 70
0
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1
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3.1k
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Comment: C: Question about some features in Cytoscape.js (or D3.js)
5.5 years ago by tunl ▴ 70
0
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1
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3.1k
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Comment: C: Question about some features in Cytoscape.js (or D3.js)
5.5 years ago by tunl ▴ 70
6
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10
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3.1k
views
Question about some features in Cytoscape.js (or D3.js)
Cytoscape.js D3.js network visualization
updated 5.5 years ago by 34k • written 5.5 years ago by ▴ 70
0
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1
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3.1k
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Comment: C: Question about some features in Cytoscape.js (or D3.js)
5.5 years ago by tunl ▴ 70
0
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1
reply
1.8k
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Comment: C: What exactly one "library" corresponds to in RNA-seq analysis
5.5 years ago by tunl ▴ 70
0
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1
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1.8k
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Comment: C: What exactly one "library" corresponds to in RNA-seq analysis
5.5 years ago by tunl ▴ 70
0
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1
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1.8k
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Comment: C: What tools are better than Cuffdiff for differential expression analysis
5.5 years ago by tunl ▴ 70
4
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3
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1.8k
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What tools are better than Cuffdiff for differential expression analysis
RNA-Seq differential expression analysis Cuffdiff
5.5 years ago by tunl ▴ 70
3
votes
5
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1.8k
views
What exactly one "library" corresponds to in RNA-seq analysis
RNA-Seq
5.5 years ago by tunl ▴ 70
1
vote
1
reply
2.3k
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Cuffdiff hangs at "Inspecting maps and determining fragment length distributions" step
RNA-Seq Cuffdiff
updated 5.9 years ago by 20 • written 6.0 years ago by ▴ 70
0
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0
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2.0k
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Comment: C: lncRNA gene vs. lncRNA isoform
6.0 years ago by tunl ▴ 70
7
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3
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2.0k
views
lncRNA gene vs. lncRNA isoform
RNA-Seq lncRNA isoforms transcripts GENCODE
updated 6.0 years ago by ★ 1.6k • written 6.0 years ago by ▴ 70
0
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0
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2.0k
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Comment: C: What determines which tests are performed in Cuffdiff? Only two types of tests w
6.0 years ago by tunl ▴ 70
0
votes
1
reply
2.0k
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Comment: C: What determines which tests are performed in Cuffdiff? Only two types of tests w
6.0 years ago by tunl ▴ 70
0
votes
1
reply
2.0k
views
Comment: C: What determines which tests are performed in Cuffdiff? Only two types of tests w
6.0 years ago by tunl ▴ 70
0
votes
0
replies
1.8k
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How important is --frag-bias-correct in running Cuffdiff (it makes Cuffdiff very slow in our case)?
RNA-Seq Cuffdiff
6.0 years ago by tunl ▴ 70
0
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0
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1.4k
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What original Cuffdiff steps does Cuffquant cover?
RNA-Seq Cuffquant Cuffdiff
6.0 years ago by tunl ▴ 70
0
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1
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2.9k
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Comment: C: Is there any fixed limit on the number of threads in running Tophat?
6.0 years ago by tunl ▴ 70
0
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1
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2.9k
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Comment: C: Is there any fixed limit on the number of threads in running Tophat?
6.0 years ago by tunl ▴ 70
0
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1
reply
2.9k
views
Comment: C: Is there any fixed limit on the number of threads in running Tophat?
6.0 years ago by tunl ▴ 70
6
votes
10
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2.9k
views
Is there any fixed limit on the number of threads in running Tophat?
RNA-Seq Tophat
updated 6.0 years ago by ★ 2.1k • written 6.0 years ago by ▴ 70
0
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0
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3.2k
views
Comment: C: Trimmomatic: Does it matter to trim the fastq before or after merging multiple r
6.0 years ago by tunl ▴ 70
6
votes
3
replies
3.2k
views
Trimmomatic: Does it matter to trim the fastq before or after merging multiple replicates?
RNA-Seq Trimmomatic
updated 6.0 years ago by 46k • written 6.0 years ago by ▴ 70
0
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0
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2.8k
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Comment: C: Read pairing issues detected in Tophat run
6.1 years ago by tunl ▴ 70
1
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1
reply
2.1k
views
FastQC report: should we not use the fastq data for Tophat+Cuffdiff if any of its modules is marked as "red cross"?
RNA-Seq FastQC Tophat Cuffdiff
6.1 years ago by tunl ▴ 70
0
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0
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4.4k
views
Comment: C: Cuffdiff takes extremely long time at "Testing for differential expression and r
6.1 years ago by tunl ▴ 70
0
votes
1
reply
2.8k
views
Comment: C: Read pairing issues detected in Tophat run
6.1 years ago by tunl ▴ 70
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