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Warning: no reference transcripts were found when map the reads to reference sequences by using stringtie
stringtie rna-seq written 8 months ago by Yuyin110 • 10 • updated 6 days ago by Asbesto • 0
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HISAT2-StringTie-CuffDiff "Sam file doesn't appear to be correctly sorted"
stringtie cuffdiff rna-seq hisat2 written 24 days ago by aboyher • 0 • updated 24 days ago by JJ • 300
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183
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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 7 weeks ago by beginner • 20 • updated 7 weeks ago by h.mon ♦ 14k
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182
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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 7 weeks ago by bryce.kirby • 0 • updated 7 weeks ago by Kevin Blighe ♦ 19k
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Stringtie prepDE.py Error line 32
stringtie deseq2 ballgown rna-seq prepde.py written 7 weeks ago by bryce.kirby • 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 9 weeks ago by nancy • 30
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minimum recommended length for transcript prediction -Stringtie
stringtie pe rna-seq written 10 weeks ago by amy16 • 20
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156
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Stringtie GTF naming convention error
gtf stringtie naming convention written 10 weeks ago by emcc • 10
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Please adivse me on differential expression analysis on the STAR/Stringtie output
count stringtie star differential expression edger written 15 months ago by seta • 970 • updated 10 weeks ago by Biostar ♦♦ 20
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150
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FPKM values all 0 from Stringtie
stringtie rna-seq written 3 months ago by jammydodger123456 • 0
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1
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276
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1
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StringTie error: list index out of range
stringtie galaxy error written 3 months ago by nazaninhoseinkhan • 210
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2
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257
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StringTie cannot be run as a problem in naming convention
gtf stringtie gene naming convention written 3 months ago by nazaninhoseinkhan • 210 • updated 3 months ago by jean.elbers • 170
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358
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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 3 months ago by beginner • 20 • updated 3 months ago by Devon Ryan ♦ 79k
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Stringtie/Cufflinks with yeast RNAseq
stringtie cufflinks rna-seq gffcompare cuffcompare written 3 months ago by grant.hovhannisyan • 780
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654
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Calculating the gene coverage in StringTie
gene stringtie coverage rna-seq written 10 months ago by sjbasu • 30 • updated 3 months ago by geo.pertea • 60
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Cuffcompare on the merged GTF file produced by Stringtie
stringtie cufflinks cuffdiff splicing written 14 months ago by seta • 970 • updated 4 months ago by Biostar ♦♦ 20
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249
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1
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Estimating the abundance of the transcripts and genes using stringtie
stringtie rna-seq written 4 months ago by amy16 • 20 • updated 4 months ago by Devon Ryan ♦ 79k
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251
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Clarification in the workflow steps of the RNA-seq analysis for differential gene analysis
assembly stringtie tuxedo rna-seq written 4 months ago by amy16 • 20
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994
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Warning encountered while transcript abundance estimation using stringtie
stringtie rna-seq abundance written 13 months ago by Vijay Lakhujani • 2.1k • updated 4 months ago by geo.pertea • 60
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7 follow
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stringtie cannot recognize Gencode GTF
stringtie rna-seq gencode written 4 months ago by dec986 • 90 • updated 4 months ago by geo.pertea • 60
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Converting MSTRG from stringtie with gene name
stringtie rna-seq written 4 months ago by fhassanz • 10 • updated 4 months ago by Biostar ♦♦ 20
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Differential gene expression anaylsis -Ballgown
ballgown stringtie rna-seq written 4 months ago by amy16 • 20 • updated 4 months ago by Hussain Ather • 860
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223
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transcript count after string tie merge
stringtie rna-seq written 4 months ago by rthapa • 0 • updated 4 months ago by Kevin Blighe ♦ 19k
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how to find novel genes and transcripts in gffcompare?
stringtie rna-seq gffcompare written 4 months ago by naveenkumarv40 • 10
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6 follow
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Regarding getting gene count tables for DeSeq from StringTie using prepDE.py
stringtie rna-seq written 8 months ago by pixie@bioinfo • 1.3k • updated 4 months ago by Saeed • 0
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349
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Issue with StringTie to get gene_count matrix for DeSEQ
stringtie rna-seq written 5 months ago by pixie@bioinfo • 1.3k • updated 5 months ago by toralmanvar • 290
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396
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stringtie + ballgown for multivariate analysis of rna-seq data
stringtie ballgown rna-seq multivariate written 5 months ago by nancy • 30
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316
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Stringtie output for DGE
stringtie ballgown written 6 months ago by amy16 • 20
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342
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Transcriptome Assembly Quastions
transcriptome assembly stringtie rna-seq written 7 months ago by tawares07 • 0 • updated 7 months ago by Kevin Blighe ♦ 19k
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StringTie "missing header error" [for both HISAT2 and STAR alignment files]
stringtie alignment tool rna-seq written 8 months ago by EagleEye • 5.1k
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