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2
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1
answer
980
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1
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can i use tophat for ribo-seq data sets
ribo-seq tophat alignment written 3.4 years ago by F • 3.2k • updated 3 days ago by Biostar ♦♦ 20
5
votes
2
answers
159
views
2
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batch effect in RNAseq analysis using tophat cufflinks pipeline
tophat cufflink rna-seq batch effect written 7 days ago by yff • 0 • updated 7 days ago by kristoffer.vittingseerup • 1.2k
3
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1
answer
2.5k
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5 follow
1
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What causes tophat_reports error?
tophat rna-seq written 4.6 years ago by Bharat Iyengar • 260 • updated 23 days ago by Biostar ♦♦ 20
1
vote
1
answer
132
views
1
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What is the reason for big difference in DEGs estimation compared to previous estimation?
tophat degs rna-seq written 5 weeks ago by anc.informatics • 0 • updated 5 weeks ago by jared.andrews07 • 1.8k
1
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0
answers
150
views
0
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tophat running does not complete properly.
tophat alignment rna-seq bowtie written 7 weeks ago by yff • 0
4
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1
answer
209
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1
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Please tell me what's wrong with my tophat script?
bowtie2 tophat bowtie1 written 10 weeks ago by abdul.suboor123 • 0 • updated 10 weeks ago by WouterDeCoster ♦ 35k
5
votes
1
answer
270
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5 follow
1
answer
Tophat2 or STAR for IsoformSwitchAnalyzeR analysis
tophat cufflinks cuffdiff star written 3 months ago by sbbinfo • 10 • updated 3 months ago by kristoffer.vittingseerup • 1.2k
7
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0
answers
274
views
0
answers
Transcriptome analysis using tophat and bowtie
software error bowtieindex tophat bowtie written 4 months ago by NAVID.BAVI • 0 • updated 4 months ago by RamRS ♦ 20k
6
votes
1
answer
313
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1
answer
Problem mapping with STAR
tophat star hisat2 written 4 months ago by alvarocentron91 • 0 • updated 4 months ago by WouterDeCoster ♦ 35k
4
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7
answers
5.2k
views
7 follow
7
answers
Write Failure In Tophat 1.3.1 X86_64
tophat splicing sequencing written 7.5 years ago by Gabrielw • 60 • updated 4 months ago by RamRS ♦ 20k
1
vote
2
answers
345
views
2
answers
Difference between two count table that created from same fastq files?
gtf tophat featurecounts rna-seq counttable written 4 months ago by cilgaiscan • 30 • updated 4 months ago by h.mon ♦ 22k
1
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0
answers
274
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0
answers
TopHat Error: Couldn't build bowtie index with err = -11
tophat rna-seq bowtie written 5 months ago by Sun Jiji • 0
0
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1
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1.6k
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1
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why i cant have sam, sorted bam or bed by tophat output?
tophat bam written 3.4 years ago by F • 3.2k • updated 5 months ago by WouterDeCoster ♦ 35k
4
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1
answer
286
views
1
answer
Different version of Tophat gives me different number of mapped reads
tophat alignment rna-seq written 5 months ago by BioDH • 0 • updated 5 months ago by swbarnes2 ♦ 4.7k
0
votes
0
answers
185
views
0
answers
Tophat2 Aligning extremely short reads
tophat alignment rna-seq sequencing written 6 months ago by biogirl04 • 0 • updated 5 months ago by Biostar ♦♦ 20
2
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0
answers
2.4k
views
0
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tophat failed: Warning: junction database is empty!
tophat mapping written 3.9 years ago by biolab • 1.1k • updated 5 months ago by Biostar ♦♦ 20
1
vote
2
answers
3.4k
views
5 follow
2
answers
How To Plot Rarefaction/Saturation Curve Based On Bam File Generated By Tophat?
tophat written 5.6 years ago by huangqp1984 • 10 • updated 5 months ago by achamess • 40
0
votes
1
answer
241
views
1
answer
extract one-side unmapped reads from sam
tophat bam samtools sam written 7 months ago by liorglic • 40 • updated 7 months ago by Carlo Yague • 4.4k
5
votes
1
answer
5.0k
views
6 follow
1
answer
tophat, the parameter "Expected inner distance between mate pairs"?
tophat expected inner distance between mate pairs written 4.0 years ago by lin.pei26 • 60 • updated 7 months ago by Biostar ♦♦ 20
0
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2
answers
716
views
2
answers
How to check if the mapping results from tophat2 are correct?
tophat mapping rna-seq written 2.4 years ago by mirza • 80 • updated 8 months ago by Biostar ♦♦ 20
0
votes
1
answer
288
views
1
answer
Tophat running error
tophat rna-seq written 8 months ago by mahnazkiani • 40 • updated 8 months ago by genomax ♦ 60k
1
vote
1
answer
339
views
5 follow
1
answer
comparing mapping statistics on s. pombe alignment (Star vs. tophat)
tophat alignment rna-seq pombe star written 9 months ago by dho322 • 0 • updated 9 months ago by Michael Dondrup ♦ 45k
1
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0
answers
251
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0
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The problem about tophat software -G parameter
tophat alignment rna-seq written 9 months ago by Wayne Lee • 10
0
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0
answers
473
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0
answers
Reducing error bars on TopHat RNA expression analysis
R tophat rna-seq bowtie written 13 months ago by waterspring • 0 • updated 9 months ago by Biostar ♦♦ 20
8
votes
1
answer
453
views
1
answer
Tophat not installing with Biostar Handbook
tophat blast from the past: the tuxedo suite written 9 months ago by k.e.pendleton • 20 • updated 9 months ago by h.mon ♦ 22k
3
votes
0
answers
466
views
0
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Tophat Error: Make in Mac OSX
tophat make rna-seq written 9 months ago by vharshavardhanan • 30 • updated 9 months ago by RamRS ♦ 20k
7
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2
answers
1.3k
views
5 follow
2
answers
TopHat installation error
tophat written 20 months ago by salamandra • 180 • updated 12 months ago by Bilal • 30
0
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1
answer
844
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1
answer
RNA SEQ ERCC
ercc tophat rna-seq bowtie written 12 months ago by Payal • 30
3
votes
1
answer
793
views
1
answer
Why different rna-seq aligners need to be used for Ion Torrent data compared with illumina?
tophat bbmap mira rna-seq hisat2 written 12 months ago by Bioinfo • 270 • updated 12 months ago by h.mon ♦ 22k
2
votes
1
answer
1.5k
views
1
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TopHat Failed In 'Reporting output tracks' Stage
software error tophat tophat2 rna-seq written 2.1 years ago by ivan.molodtsov • 10 • updated 12 months ago by zuolin.bai • 0
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