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11
votes
1
answer
208
views
7 follow
1
answer
TopHat mapping error
tophat bowtie rna-seq written 14 days ago by gokberk • 0 • updated 13 days ago by genomax ♦ 65k
0
votes
2
answers
125
views
5 follow
2
answers
Directional Strand related settings for RNA-seq Analysis Software
htseq tophat rna-seq smartseq hisat2 written 16 days ago by BM • 40 • updated 16 days ago by Juke-34 • 2.1k
0
votes
2
answers
2.5k
views
2
answers
Tophat Error - What Does This Mean?
tophat error bowtie written 5.7 years ago by newDNASeqer • 630 • updated 18 days ago by Biostar ♦♦ 20
19
votes
6
answers
416
views
7 follow
6
answers
Tophat vs Bowtie alignment rates
bowtie2 tophat alignment written 7 weeks ago by am3 • 70
10
votes
1
answer
236
views
1
answer
why reads align to other coordinates?
bowtie2 tophat alignment rna-seq align written 12 weeks ago by star • 140
2
votes
1
answer
1.1k
views
1
answer
can i use tophat for ribo-seq data sets
ribo-seq tophat alignment written 3.6 years ago by F • 3.4k • updated 3 months ago by Biostar ♦♦ 20
5
votes
2
answers
317
views
2
answers
batch effect in RNAseq analysis using tophat cufflinks pipeline
tophat cufflink rna-seq batch effect written 3 months ago by yff • 0 • updated 3 months ago by kristoffer.vittingseerup • 1.7k
3
votes
1
answer
2.6k
views
5 follow
1
answer
What causes tophat_reports error?
tophat rna-seq written 4.9 years ago by Bharat Iyengar • 260 • updated 3 months ago by Biostar ♦♦ 20
1
vote
1
answer
214
views
1
answer
What is the reason for big difference in DEGs estimation compared to previous estimation?
tophat degs rna-seq written 4 months ago by anc.informatics • 0 • updated 4 months ago by jared.andrews07 • 2.2k
1
vote
0
answers
225
views
0
answers
tophat running does not complete properly.
tophat alignment rna-seq bowtie written 4 months ago by yff • 0
4
votes
1
answer
308
views
1
answer
Please tell me what's wrong with my tophat script?
bowtie2 tophat bowtie1 written 5 months ago by abdul.suboor123 • 0 • updated 5 months ago by WouterDeCoster ♦ 38k
5
votes
1
answer
414
views
5 follow
1
answer
Tophat2 or STAR for IsoformSwitchAnalyzeR analysis
tophat cufflinks cuffdiff star written 6 months ago by sbb • 10 • updated 6 months ago by kristoffer.vittingseerup • 1.7k
7
votes
0
answers
437
views
0
answers
Transcriptome analysis using tophat and bowtie
software error bowtieindex tophat bowtie written 7 months ago by NAVID.BAVI • 0 • updated 7 months ago by RamRS ♦ 21k
6
votes
1
answer
448
views
1
answer
Problem mapping with STAR
tophat star hisat2 written 7 months ago by alvarocentron91 • 10 • updated 7 months ago by WouterDeCoster ♦ 38k
4
votes
7
answers
5.3k
views
7 follow
7
answers
Write Failure In Tophat 1.3.1 X86_64
tophat splicing sequencing written 7.8 years ago by Gabrielw • 60 • updated 7 months ago by RamRS ♦ 21k
1
vote
2
answers
443
views
2
answers
Difference between two count table that created from same fastq files?
gtf tophat featurecounts rna-seq counttable written 7 months ago by cilgaiscan • 50 • updated 7 months ago by h.mon ♦ 24k
1
vote
0
answers
381
views
0
answers
TopHat Error: Couldn't build bowtie index with err = -11
tophat rna-seq bowtie written 8 months ago by Sun Jiji • 0
0
votes
1
answer
1.8k
views
1
answer
why i cant have sam, sorted bam or bed by tophat output?
tophat bam written 3.6 years ago by F • 3.4k • updated 8 months ago by WouterDeCoster ♦ 38k
4
votes
1
answer
368
views
1
answer
Different version of Tophat gives me different number of mapped reads
tophat alignment rna-seq written 8 months ago by BioDH • 0 • updated 8 months ago by swbarnes2 ♦ 5.2k
0
votes
0
answers
234
views
0
answers
Tophat2 Aligning extremely short reads
tophat alignment rna-seq sequencing written 9 months ago by biogirl04 • 0 • updated 8 months ago by Biostar ♦♦ 20
2
votes
0
answers
2.5k
views
0
answers
tophat failed: Warning: junction database is empty!
tophat mapping written 4.1 years ago by biolab • 1.1k • updated 8 months ago by Biostar ♦♦ 20
1
vote
2
answers
3.5k
views
5 follow
2
answers
How To Plot Rarefaction/Saturation Curve Based On Bam File Generated By Tophat?
tophat written 5.9 years ago by huangqp1984 • 10 • updated 9 months ago by achamess • 40
0
votes
1
answer
358
views
1
answer
extract one-side unmapped reads from sam
tophat bam samtools sam written 10 months ago by liorglic • 50 • updated 10 months ago by Carlo Yague • 4.4k
5
votes
1
answer
5.2k
views
6 follow
1
answer
tophat, the parameter "Expected inner distance between mate pairs"?
tophat expected inner distance between mate pairs written 4.2 years ago by lin.pei26 • 70 • updated 10 months ago by Biostar ♦♦ 20
0
votes
2
answers
766
views
2
answers
How to check if the mapping results from tophat2 are correct?
tophat mapping rna-seq written 2.7 years ago by mirza • 80 • updated 11 months ago by Biostar ♦♦ 20
0
votes
1
answer
386
views
1
answer
Tophat running error
tophat rna-seq written 11 months ago by mahnazkiani • 40 • updated 11 months ago by genomax ♦ 65k
1
vote
1
answer
410
views
5 follow
1
answer
comparing mapping statistics on s. pombe alignment (Star vs. tophat)
tophat alignment rna-seq pombe star written 12 months ago by dho322 • 0 • updated 12 months ago by Michael Dondrup ♦ 46k
1
vote
0
answers
325
views
0
answers
The problem about tophat software -G parameter
tophat alignment rna-seq written 12 months ago by Wayne Lee • 10
0
votes
0
answers
542
views
0
answers
Reducing error bars on TopHat RNA expression analysis
R tophat rna-seq bowtie written 16 months ago by waterspring • 0 • updated 12 months ago by Biostar ♦♦ 20
8
votes
1
answer
566
views
1
answer
Tophat not installing with Biostar Handbook
tophat blast from the past: the tuxedo suite written 12 months ago by k.e.pendleton • 20 • updated 12 months ago by h.mon ♦ 24k
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