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4
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StringTie giving different results - same dataset
rnaseq stringtie denovo transcript assembly written 6 days ago by raquelgarza95 • 10
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1
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80
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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 11 days ago by ever_wudi • 10
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0
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75
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Stringtie merge generates close duplicates of original transcripts
stringtie written 23 days ago by jammydodger123456 • 10
2
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0
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423
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0
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how to find novel genes and transcripts in gffcompare?
stringtie rna-seq gffcompare written 7 months ago by naveenkumarv40 • 20 • updated 4 weeks ago by geek_y ♦ 8.7k
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81
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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 4 weeks ago by tawares07 • 0
2
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178
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Stringtie output gtf file only contains STRG transripts, no original annotations
stringtie written 10 weeks ago by jammydodger123456 • 10
1
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1
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150
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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 7 weeks ago by Farbod • 3.1k • updated 7 weeks ago by Vijay Lakhujani ♦ 3.0k
0
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129
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Unknown Stringtie IDs produced when using Ensembl GTF
gtf ensembl stringtie rna-seq written 8 weeks ago by freuv • 20 • updated 8 weeks ago by Emily_Ensembl ♦ 15k
1
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1
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239
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1
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Stringtie output files
gtf stringtie rna-seq written 9 weeks ago by g.e.novakovsky • 10 • updated 8 weeks ago by Kevin Blighe ♦ 25k
11
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1
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196
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7 follow
1
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How many genes in RNA seq?
stringtie rna-seq written 10 weeks ago by ag1805x • 90
2
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1
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200
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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 11 weeks ago by akilabioinfo • 0 • updated 11 weeks ago by Devon Ryan ♦ 82k
5
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1
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479
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1
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Stringtie prepDE.py Error line 32
stringtie deseq2 ballgown rna-seq prepde.py written 4 months ago by bryce.kirby • 0 • updated 12 weeks ago by Biostar ♦♦ 20
1
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1
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208
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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 12 weeks ago by Biologist • 70 • updated 12 weeks ago by Kevin Blighe ♦ 25k
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1
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939
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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 11 months ago by Yuyin110 • 10 • updated 3 months ago by Asbesto • 0
0
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1
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226
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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 3 months ago by aboyher • 0 • updated 3 months ago by JJ • 320
2
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361
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0
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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 4 months ago by Biologist • 70 • updated 4 months ago by h.mon ♦ 18k
3
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1
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338
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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 4 months ago by bryce.kirby • 0 • updated 4 months ago by Kevin Blighe ♦ 25k
0
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239
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0
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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 5 months ago by nancy • 60
1
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246
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minimum recommended length for transcript prediction -Stringtie
stringtie pe rna-seq written 5 months ago by amy16 • 30
1
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0
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232
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0
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Stringtie GTF naming convention error
gtf stringtie naming convention written 5 months ago by emcc • 10
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2
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1.7k
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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 18 months ago by seta • 1000 • updated 5 months ago by Biostar ♦♦ 20
1
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0
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210
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0
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FPKM values all 0 from Stringtie
stringtie rna-seq written 6 months ago by jammydodger123456 • 10
0
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1
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479
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1
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StringTie error: list index out of range
stringtie galaxy error written 6 months ago by nazaninhoseinkhan • 250
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2
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378
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2
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StringTie cannot be run as a problem in naming convention
gtf stringtie gene naming convention written 6 months ago by nazaninhoseinkhan • 250 • updated 6 months ago by jean.elbers • 340
4
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1
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578
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1
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Stringtie with Gencode gtf file doesn't give any gene_ids or transcript_ids?
gtf stringtie rna-seq gencode lncrna written 6 months ago by Biologist • 70 • updated 6 months ago by Devon Ryan ♦ 82k
1
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0
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270
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0
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Stringtie/Cufflinks with yeast RNAseq
stringtie cufflinks rna-seq gffcompare cuffcompare written 6 months ago by grant.hovhannisyan • 990
5
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1
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942
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1
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Calculating the gene coverage in StringTie
gene stringtie coverage rna-seq written 13 months ago by sjbasu • 30 • updated 6 months ago by geo.pertea • 60
0
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757
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Cuffcompare on the merged GTF file produced by Stringtie
stringtie cufflinks cuffdiff splicing written 16 months ago by seta • 1000 • updated 7 months ago by Biostar ♦♦ 20
1
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1
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377
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1
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Estimating the abundance of the transcripts and genes using stringtie
stringtie rna-seq written 7 months ago by amy16 • 30 • updated 7 months ago by Devon Ryan ♦ 82k
0
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310
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0
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Clarification in the workflow steps of the RNA-seq analysis for differential gene analysis
assembly stringtie tuxedo rna-seq written 7 months ago by amy16 • 30
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