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Comment: C: Samtofastq: Net.Sf.Picard.Picardexception: "Found N Unpaired Mates "
updated 5.4 years ago by 45k • written 10.7 years ago by ▴ 160
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3.5k
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Comment: Comment: how to export RNA-seq reads which mapped to genes?
updated 4.1 years ago by 45k • written 10.5 years ago by ▴ 160
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0
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3.5k
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Comment: Comment: how to export RNA-seq reads which mapped to genes?
updated 4.1 years ago by 45k • written 10.5 years ago by ▴ 160
0
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0
replies
3.5k
views
Comment: Comment: how to export RNA-seq reads which mapped to genes?
updated 4.1 years ago by 45k • written 10.5 years ago by ▴ 160
0
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1
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3.5k
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Comment: Comment: how to export RNA-seq reads which mapped to genes?
updated 4.1 years ago by 45k • written 10.5 years ago by ▴ 160
0
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1
reply
2.3k
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total-hits-norm and compatible-hits-norm default setting different in Cufflinks and Cuffdiff
RNA-Seq Cufflinks Cuffdiff
7.1 years ago by trakhtenberg ▴ 160
6
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2
replies
3.7k
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Comparing Fpkm values from samples processed in same or different runs using tophat/cufflinks
rna-seq
updated 8.0 years ago by 20 • written 10.7 years ago by ▴ 160
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0
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2.4k
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Comment: C: Does upper-quartile normalization in Cuffdiff also normalizes by transcript leng
8.9 years ago by trakhtenberg ▴ 160
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0
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3.1k
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Upper-quartile normalization option for Cufflinks and Cuffdiff
Cufflinks Cuffdiff Upper-quartile normalization
8.9 years ago by trakhtenberg ▴ 160
1
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2
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2.4k
views
Does upper-quartile normalization in Cuffdiff also normalizes by transcript length?
RNA-Seq Cuffdiff Upper-quartile normalization
updated 8.9 years ago by 13k • written 8.9 years ago by ▴ 160
5
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4
replies
3.8k
views
How to identify with Tophat maximum number of uniquely aligned reads by allowing mismatches only conditionally?
RNA-Seq
updated 3.3 years ago by 45k • written 10.7 years ago by ▴ 160
0
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1
reply
4.0k
views
GOseq and KEGG pathways analysis for mouse RNA-seq
KEGG RNA-Seq GOseq
updated 2.9 years ago by 45k • written 10.1 years ago by ▴ 160
1
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1
reply
2.5k
views
PWF from GOseq to adjust q-value in Cuffdiff
GOseq RNA-Seq gene length bias
updated 2.9 years ago by 45k • written 10.1 years ago by ▴ 160
0
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0
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3.5k
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Comment: Comment: how to export RNA-seq reads which mapped to genes?
updated 4.1 years ago by 45k • written 10.5 years ago by ▴ 160
0
votes
0
replies
3.5k
views
Comment: Comment: how to export RNA-seq reads which mapped to genes?
updated 4.1 years ago by 45k • written 10.5 years ago by ▴ 160
0
votes
2
replies
3.5k
views
Comment: Comment: how to export RNA-seq reads which mapped to genes?
updated 4.1 years ago by 45k • written 10.5 years ago by ▴ 160
3
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16
replies
3.5k
views
how to export RNA-seq reads which mapped to genes?
RNA-Seq
updated 3.3 years ago by 45k • written 10.5 years ago by ▴ 160
0
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1
reply
3.5k
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Comment: Comment: how to export RNA-seq reads which mapped to genes?
updated 4.1 years ago by 45k • written 10.5 years ago by ▴ 160
0
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6
replies
5.3k
views
Converting BAM to Fastq with HTSlib htscmd
Fastq Bam2Fastq Tophat BAM HTSlib
updated 3.3 years ago by 45k • written 10.7 years ago by ▴ 160
0
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1
reply
3.4k
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sorting merged GTFs for Tophat/Cufflinks pipeline
GTF Cufflinks
10.6 years ago by trakhtenberg ▴ 160
0
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0
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8.8k
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Comment: C: How to reduce reads in fastq, bam, bed files in a random manner?
10.7 years ago by trakhtenberg ▴ 160
0
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0
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1.7k
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Which flagstat output categories are passed by Tophat to Cufflinks for analysis?
flagstat Cufflinks Tophat
updated 3.3 years ago by 45k • written 10.7 years ago by ▴ 160
0
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0
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5.2k
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Comment: Comment: Picard error Illegal Mate State in converting BAM to Fastq
updated 3.3 years ago by 45k • written 10.7 years ago by ▴ 160
0
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0
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5.3k
views
Comment: C: Converting BAM to Fastq with HTSlib htscmd
10.7 years ago by trakhtenberg ▴ 160
4
votes
3
replies
5.2k
views
Picard error Illegal Mate State in converting BAM to Fastq
Picard SamToFastq BamToFastq
updated 3.3 years ago by 45k • written 10.7 years ago by ▴ 160
0
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0
replies
9.9k
views
Answer: A: Picard Exception: Illegal Mate State
10.7 years ago by trakhtenberg ▴ 160
0
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1
reply
51k
views
Comment: Comment: Fastq Splitter For Paired End Reads
updated 3.3 years ago by 45k • written 10.7 years ago by ▴ 160
0
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0
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3.8k
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Comment: Comment: How to identify with Tophat maximum number of uniquely aligned reads by allowing
updated 3.3 years ago by 45k • written 10.7 years ago by ▴ 160
0
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1
reply
3.8k
views
Comment: Comment: How to identify with Tophat maximum number of uniquely aligned reads by allowing
updated 3.3 years ago by 45k • written 10.7 years ago by ▴ 160
0
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0
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11k
views
Comment: Comment: Extracting from tophat outputs reads pairs and splice-junctions with a single be
updated 3.3 years ago by 45k • written 10.7 years ago by ▴ 160
0
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1
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11k
views
Comment: Comment: Extracting from tophat outputs reads pairs and splice-junctions with a single be
updated 3.3 years ago by 45k • written 10.7 years ago by ▴ 160
11
votes
10
replies
11k
views
Extracting from tophat outputs reads pairs and splice-junctions with a single best match
TOPHAT RNA-Seq
updated 3.3 years ago by 45k • written 10.7 years ago by ▴ 160
0
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2
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2.9k
views
Comment: C: How to convert strand-specific reads to not-strand-specific format?
10.7 years ago by trakhtenberg ▴ 160
4
votes
5
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2.9k
views
How to convert strand-specific reads to not-strand-specific format?
RNA-Seq
updated 3.4 years ago by 45k • written 10.7 years ago by ▴ 160
9
votes
9
replies
8.8k
views
6 follow
How to reduce reads in fastq, bam, bed files in a random manner?
RNA-Seq
updated 3.4 years ago by 45k • written 10.7 years ago by ▴ 160
0
votes
0
replies
12k
views
Comment: Comment: tophat output files containing the reads which mapped uniquely as a pair
updated 3.4 years ago by 45k • written 10.7 years ago by ▴ 160
4
votes
2
replies
12k
views
tophat output files containing the reads which mapped uniquely as a pair
TOPHAT RNA-Seq
updated 3.4 years ago by 45k • written 10.7 years ago by ▴ 160
0
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0
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5.1k
views
Comment: C: Identifying polyA tail sequences for predicted novel transcripts using STAR/Cuff
10.7 years ago by trakhtenberg ▴ 160
0
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0
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5.1k
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Comment: C: Identifying polyA tail sequences for predicted novel transcripts using STAR/Cuff
10.7 years ago by trakhtenberg ▴ 160
0
votes
0
replies
1.4k
views
comprehensive mouse GTF for discovery of novel transcripts? Beyond GENCODE M3
RNA-Seq
updated 10.7 years ago by 20 • written 10.7 years ago by ▴ 160
0
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1
reply
5.1k
views
Comment: Comment: Identifying polyA tail sequences for predicted novel transcripts using STAR/Cuff
updated 3.4 years ago by 45k • written 10.7 years ago by ▴ 160
0
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1
reply
5.1k
views
Comment: Comment: Identifying polyA tail sequences for predicted novel transcripts using STAR/Cuff
updated 3.4 years ago by 45k • written 10.7 years ago by ▴ 160
5
votes
8
replies
5.1k
views
Identifying polyA tail sequences for predicted novel transcripts using STAR/Cufflinks
RNA-Seq
updated 3.4 years ago by 45k • written 10.7 years ago by ▴ 160
0
votes
0
replies
2.0k
views
Best annotation GTFs for transcript detection vs novel transcript discovery
RNA-Seq
updated 3.4 years ago by 45k • written 10.7 years ago by ▴ 160
0
votes
0
replies
4.2k
views
Comment: C: Are polyA tails filtered at some step of tophat/cufflinks processing or this inf
10.7 years ago by trakhtenberg ▴ 160
0
votes
0
replies
4.2k
views
Comment: C: Are polyA tails filtered at some step of tophat/cufflinks processing or this inf
10.7 years ago by trakhtenberg ▴ 160
0
votes
1
reply
4.2k
views
Comment: Comment: Are polyA tails filtered at some step of tophat/cufflinks processing or this inf
updated 3.4 years ago by 45k • written 10.7 years ago by ▴ 160
8
votes
6
replies
4.2k
views
Are polyA tails filtered at some step of tophat/cufflinks processing or this information is retained?
RNA-Seq
updated 3.4 years ago by 45k • written 10.7 years ago by ▴ 160
0
votes
0
replies
3.7k
views
Comment: C: Comparing Fpkm values from samples processed in same or different runs using top
10.7 years ago by trakhtenberg ▴ 160
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