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Where to find a valid GTF file for stringtie asssembly?
gtf stringtie transcriptome written 2 days ago by Vijay Lakhujani ♦ 3.1k • updated 2 days ago by Damian Kao ♦ 15k
2
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1
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163
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stringtie merge error bam file not sorted
stringtie rna-seq written 17 days ago by paumarc • 10
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1
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606
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Gffread error: Error (GFaSeqGet): subsequence cannot be larger than...
stringtie gffread rna-seq written 15 months ago by jjrin • 10 • updated 16 days ago by spriyar • 0
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88
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Too Many StringTie Genes
stringtie written 26 days ago by gtasource • 20
1
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1
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123
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1
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RNA-seq samples along different time points, how to run Stringtie?
stringtie rna-seq time-point written 29 days ago by iraia.munoa • 10 • updated 28 days ago by grant.hovhannisyan • 1.1k
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464
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Estimating the abundance of the transcripts and genes using stringtie
stringtie rna-seq written 9 months ago by amy16 • 30 • updated 29 days ago by iraia.munoa • 10
2
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1
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115
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1
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How to deal with single transcripts assigned to multiple genes?
stringtie rna-seq hisat2 written 4 weeks ago by antoinefelden • 20 • updated 29 days ago by RamRS ♦ 18k
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2
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149
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5 follow
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Proper design for DESeq2 and other RNAseq general questions
stringtie deseq2 rna-seq hisat2 written 4 weeks ago by Stef • 0 • updated 4 weeks ago by swbarnes2 ♦ 4.2k
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177
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1
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FPKM matrix after stringtie using ballgown
stringtie ballgown fpkm rna-seq written 7 weeks ago by Bioinfo • 270 • updated 7 weeks ago by Adrian Pelin • 2.2k
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150
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StringTie giving different results - same dataset
rnaseq stringtie denovo transcript assembly written 9 weeks ago by raquelgarza95 • 10
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1
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150
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1
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Outputing gexpr() with gene_name (or gene symbol) instead of MSTRG.x gene_id
ballgown stringtie rna-seq gene_name written 10 weeks ago by ever_wudi • 10
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150
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Stringtie merge generates close duplicates of original transcripts
stringtie written 12 weeks ago by jammydodger123456 • 10
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how to find novel genes and transcripts in gffcompare?
stringtie rna-seq gffcompare written 9 months ago by naveenkumarv40 • 20 • updated 3 months ago by geek_y ♦ 8.7k
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142
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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 3 months ago by tawares07 • 0
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298
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Stringtie output gtf file only contains STRG transripts, no original annotations
stringtie written 4 months ago by jammydodger123456 • 10
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254
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1
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Adding tag XS to HISAT2 sam files perior to StringTie
stringtie alignment samtools rna-seq hisat2 written 3 months ago by Farbod • 3.2k • updated 3 months ago by Vijay Lakhujani ♦ 3.1k
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193
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Unknown Stringtie IDs produced when using Ensembl GTF
gtf ensembl stringtie rna-seq written 4 months ago by freuv • 20 • updated 4 months ago by Emily_Ensembl ♦ 16k
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1
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566
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1
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Stringtie output files
gtf stringtie rna-seq written 4 months ago by g.e.novakovsky • 20 • updated 4 months ago by Kevin Blighe ♦ 30k
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1
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236
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7 follow
1
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How many genes in RNA seq?
stringtie rna-seq written 4 months ago by ag1805x • 90
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1
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248
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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 4 months ago by akilabioinfo • 0 • updated 4 months ago by Devon Ryan ♦ 85k
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Stringtie prepDE.py Error line 32
stringtie deseq2 ballgown rna-seq prepde.py written 6 months ago by bryce.kirby • 0 • updated 5 months ago by Biostar ♦♦ 20
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1
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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 5 months ago by Biologist • 80 • updated 5 months ago by Kevin Blighe ♦ 30k
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1
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Warning: no reference transcripts were found when map the reads to reference sequences by using stringtie
stringtie rna-seq written 13 months ago by Yuyin110 • 10 • updated 5 months ago by Asbesto • 0
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1
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325
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1
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HISAT2-StringTie-CuffDiff "Sam file doesn't appear to be correctly sorted"
stringtie cuffdiff rna-seq hisat2 written 5 months ago by aboyher • 0 • updated 5 months ago by JJ • 360
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How to make the script work with stringtie command first and then merge the outputs?
stringtie bash merge rna-seq linux written 6 months ago by Biologist • 80 • updated 6 months ago by h.mon ♦ 20k
3
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1
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413
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1
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Differential Expression in DEseq2 to GSEA (9 samples, 3 conditions)
stringtie deseq2 rna-seq differential expression written 6 months ago by bryce.kirby • 0 • updated 6 months ago by Kevin Blighe ♦ 30k
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333
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What measure should be used to calculate fold-change while using Ballgown to compare D.E genes between 2 conditions?
ballgown stringtie rna-seq hisat2 written 7 months ago by nancy • 60
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296
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minimum recommended length for transcript prediction -Stringtie
stringtie pe rna-seq written 7 months ago by amy16 • 30
1
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0
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289
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0
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Stringtie GTF naming convention error
gtf stringtie naming convention written 7 months ago by emcc • 10
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2.1k
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2
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Please adivse me on differential expression analysis on the STAR/Stringtie output
count stringtie star differential expression edger written 20 months ago by seta • 1.0k • updated 7 months ago by Biostar ♦♦ 20
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