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2.1k
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total-hits-norm and compatible-hits-norm default setting different in Cufflinks and Cuffdiff
RNA-Seq
Cufflinks
Cuffdiff
6.1 years ago by
trakhtenberg
▴ 160
6
votes
2
replies
3.5k
views
Comparing Fpkm values from samples processed in same or different runs using tophat/cufflinks
rna-seq
updated 7.0 years ago by
Biostar
20 • written 9.7 years ago by
trakhtenberg
▴ 160
0
votes
0
replies
2.9k
views
Upper-quartile normalization option for Cufflinks and Cuffdiff
Cufflinks
Cuffdiff
Upper-quartile normalization
7.9 years ago by
trakhtenberg
▴ 160
1
vote
2
replies
2.2k
views
Does upper-quartile normalization in Cuffdiff also normalizes by transcript length?
RNA-Seq
Cuffdiff
Upper-quartile normalization
updated 7.9 years ago by
igor
13k • written 7.9 years ago by
trakhtenberg
▴ 160
5
votes
4
replies
3.5k
views
How to identify with Tophat maximum number of uniquely aligned reads by allowing mismatches only conditionally?
RNA-Seq
updated 2.3 years ago by
Ram
43k • written 9.7 years ago by
trakhtenberg
▴ 160
0
votes
1
reply
3.7k
views
GOseq and KEGG pathways analysis for mouse RNA-seq
KEGG
RNA-Seq
GOseq
updated 23 months ago by
Ram
43k • written 9.1 years ago by
trakhtenberg
▴ 160
1
vote
1
reply
2.3k
views
PWF from GOseq to adjust q-value in Cuffdiff
GOseq
RNA-Seq
gene length bias
updated 23 months ago by
Ram
43k • written 9.1 years ago by
trakhtenberg
▴ 160
3
votes
16
replies
2.8k
views
how to export RNA-seq reads which mapped to genes?
RNA-Seq
updated 2.2 years ago by
Ram
43k • written 9.5 years ago by
trakhtenberg
▴ 160
0
votes
6
replies
4.9k
views
Converting BAM to Fastq with HTSlib htscmd
Fastq
Bam2Fastq
Tophat
BAM
HTSlib
updated 2.3 years ago by
Ram
43k • written 9.6 years ago by
trakhtenberg
▴ 160
0
votes
1
reply
3.3k
views
sorting merged GTFs for Tophat/Cufflinks pipeline
GTF
Cufflinks
9.6 years ago by
trakhtenberg
▴ 160
0
votes
0
replies
1.6k
views
Which flagstat output categories are passed by Tophat to Cufflinks for analysis?
flagstat
Cufflinks
Tophat
updated 2.3 years ago by
Ram
43k • written 9.6 years ago by
trakhtenberg
▴ 160
4
votes
3
replies
4.8k
views
Picard error Illegal Mate State in converting BAM to Fastq
Picard
SamToFastq
BamToFastq
updated 2.3 years ago by
Ram
43k • written 9.6 years ago by
trakhtenberg
▴ 160
11
votes
10
replies
10k
views
Extracting from tophat outputs reads pairs and splice-junctions with a single best match
TOPHAT
RNA-Seq
updated 2.3 years ago by
Ram
43k • written 9.7 years ago by
trakhtenberg
▴ 160
4
votes
5
replies
2.6k
views
How to convert strand-specific reads to not-strand-specific format?
RNA-Seq
updated 2.3 years ago by
Ram
43k • written 9.7 years ago by
trakhtenberg
▴ 160
9
votes
9
replies
8.0k
views
6 follow
How to reduce reads in fastq, bam, bed files in a random manner?
RNA-Seq
updated 2.3 years ago by
Ram
43k • written 9.7 years ago by
trakhtenberg
▴ 160
4
votes
2
replies
11k
views
tophat output files containing the reads which mapped uniquely as a pair
TOPHAT
RNA-Seq
updated 2.3 years ago by
Ram
43k • written 9.7 years ago by
trakhtenberg
▴ 160
0
votes
0
replies
1.3k
views
comprehensive mouse GTF for discovery of novel transcripts? Beyond GENCODE M3
RNA-Seq
updated 9.7 years ago by
Biostar
20 • written 9.7 years ago by
trakhtenberg
▴ 160
5
votes
8
replies
4.5k
views
Identifying polyA tail sequences for predicted novel transcripts using STAR/Cufflinks
RNA-Seq
updated 2.4 years ago by
Ram
43k • written 9.7 years ago by
trakhtenberg
▴ 160
0
votes
0
replies
1.8k
views
Best annotation GTFs for transcript detection vs novel transcript discovery
RNA-Seq
updated 2.4 years ago by
Ram
43k • written 9.7 years ago by
trakhtenberg
▴ 160
8
votes
6
replies
3.7k
views
Are polyA tails filtered at some step of tophat/cufflinks processing or this information is retained?
RNA-Seq
updated 2.4 years ago by
Ram
43k • written 9.7 years ago by
trakhtenberg
▴ 160
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