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2
votes
1
answer
156
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1
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What's the difference of FPKM generated by htseq and stringtie?
htseq fpkm stringtie written 17 days ago by hxlei613 • 80 • updated 17 days ago by Devon Ryan ♦ 86k
0
votes
0
answers
81
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0
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Expression data from cufflinks merged gtf
bedtools gtf stringtie rna-seq written 19 days ago by ddowlin • 70
0
votes
1
answer
117
views
1
answer
'gene_name' is missing in StringTie output file 't_data.ctab'
stringtie deseq2 new tuxedo protocol rna-seq written 25 days ago by swarajgaikwad15 • 0 • updated 24 days ago by Viswanathan • 0
0
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1
answer
124
views
1
answer
Hisat2 output for stringtie
stringtie hisat2 written 26 days ago by Sam • 80 • updated 25 days ago by Vijay Lakhujani ♦ 3.4k
0
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1
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125
views
1
answer
Error in running DESeqDataSetFromTximport
tximport R stringtie deseq2 rna-seq written 29 days ago by ankur • 0 • updated 29 days ago by Devon Ryan ♦ 86k
2
votes
1
answer
153
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1
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Unable to create file for tximport
tximport stringtie deseq2 rna-seq written 4 weeks ago by ankur • 0 • updated 4 weeks ago by kristoffer.vittingseerup • 1.0k
3
votes
2
answers
151
views
2
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How to compare kallisto and stringtie output
stringtie next-gen kallisto rna-seq sequencing written 4 weeks ago by yusuf.zhc • 0 • updated 4 weeks ago by kristoffer.vittingseerup • 1.0k
4
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0
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189
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6 follow
0
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Error in prepDE.py in Tuxedo protocol after StringTie quantification
stringtie deseq2 new tuxedo protocol rna-seq written 4 weeks ago by swarajgaikwad15 • 0 • updated 4 weeks ago by WouterDeCoster ♦ 35k
0
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1
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132
views
1
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Where to find a valid GTF file for stringtie asssembly?
gtf stringtie transcriptome written 8 weeks ago by Vijay Lakhujani ♦ 3.4k • updated 8 weeks ago by Damian Kao ♦ 15k
2
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1
answer
282
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1
answer
stringtie merge error bam file not sorted
stringtie rna-seq written 10 weeks ago by paumarc • 10
1
vote
1
answer
689
views
1
answer
Gffread error: Error (GFaSeqGet): subsequence cannot be larger than...
stringtie gffread rna-seq written 17 months ago by jjrin • 10 • updated 10 weeks ago by spriyar • 10
1
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0
answers
141
views
0
answers
Too Many StringTie Genes
stringtie written 12 weeks ago by gtasource • 20
1
vote
1
answer
176
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1
answer
RNA-seq samples along different time points, how to run Stringtie?
stringtie rna-seq time-point written 12 weeks ago by iraia.munoa • 10 • updated 12 weeks ago by grant.hovhannisyan • 1.3k
1
vote
1
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532
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1
answer
Estimating the abundance of the transcripts and genes using stringtie
stringtie rna-seq written 11 months ago by amy16 • 30 • updated 12 weeks ago by iraia.munoa • 10
2
votes
1
answer
174
views
1
answer
How to deal with single transcripts assigned to multiple genes?
stringtie rna-seq hisat2 written 3 months ago by antoinefelden • 20 • updated 12 weeks ago by RamRS ♦ 19k
2
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2
answers
222
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5 follow
2
answers
Proper design for DESeq2 and other RNAseq general questions
stringtie deseq2 rna-seq hisat2 written 3 months ago by Stef • 0 • updated 3 months ago by swbarnes2 ♦ 4.6k
2
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1
answer
307
views
1
answer
FPKM matrix after stringtie using ballgown
stringtie ballgown fpkm rna-seq written 3 months ago by Bioinfo • 270 • updated 3 months ago by Adrian Pelin • 2.2k
4
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0
answers
179
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0
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StringTie giving different results - same dataset
rnaseq stringtie denovo transcript assembly written 4 months ago by raquelgarza95 • 10
0
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1
answer
225
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1
answer
Outputing gexpr() with gene_name (or gene symbol) instead of MSTRG.x gene_id
ballgown stringtie rna-seq gene_name written 4 months ago by ever_wudi • 10
0
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0
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188
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0
answers
Stringtie merge generates close duplicates of original transcripts
stringtie written 4 months ago by jammydodger123456 • 10
2
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0
answers
716
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0
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how to find novel genes and transcripts in gffcompare?
stringtie rna-seq gffcompare written 11 months ago by naveenkumarv40 • 20 • updated 5 months ago by geek_y ♦ 8.8k
0
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0
answers
186
views
0
answers
How can I know if a new transcript was assembled in a specific or both conditions in merge GTF file?
find new assemblies stringtie merge protocol written 5 months ago by tawares07 • 0
2
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0
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450
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0
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Stringtie output gtf file only contains STRG transripts, no original annotations
stringtie written 6 months ago by jammydodger123456 • 10
1
vote
1
answer
335
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1
answer
Adding tag XS to HISAT2 sam files perior to StringTie
stringtie alignment samtools rna-seq hisat2 written 5 months ago by Farbod • 3.2k • updated 5 months ago by Vijay Lakhujani ♦ 3.4k
0
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0
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253
views
0
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Unknown Stringtie IDs produced when using Ensembl GTF
gtf ensembl stringtie rna-seq written 6 months ago by freuv • 20 • updated 6 months ago by Emily_Ensembl ♦ 16k
1
vote
1
answer
739
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1
answer
Stringtie output files
gtf stringtie rna-seq written 6 months ago by g.e.novakovsky • 20 • updated 6 months ago by Kevin Blighe ♦ 33k
11
votes
1
answer
287
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7 follow
1
answer
How many genes in RNA seq?
stringtie rna-seq written 6 months ago by ag1805x • 120
2
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1
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290
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1
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Differential gene expression results are different while using hg19 and hg38 genomic assembly
stringtie galaxy featurecounts cufflink rna-seq written 6 months ago by akilabioinfo • 0 • updated 6 months ago by Devon Ryan ♦ 86k
5
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1
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1.1k
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1
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Stringtie prepDE.py Error line 32
stringtie deseq2 ballgown rna-seq prepde.py written 8 months ago by bryce.kirby • 0 • updated 6 months ago by Biostar ♦♦ 20
1
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1
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592
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1
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stringtie merged gtf doesn't give any gene expression columns
stringtie merge rna-seq hisat2 written 7 months ago by Biologist • 110 • updated 7 months ago by Kevin Blighe ♦ 33k
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