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140
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How to obtain transcript level TPM using stringtie?
stringtie rna-seq written 10 days ago by kousi31 • 0 • updated 6 days ago by ruisergioluis • 20
0
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0
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107
views
0
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Processing RNA-seq expression for inter sample classification
stringtie classification rna-seq dge written 6 weeks ago by SJ Basu • 30
3
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0
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217
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6 follow
0
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Can I ignore these MSTRG genes in downstream analysis (pantherdb.org)?
stringtie deseq2 rna-seq written 11 weeks ago by Fawzi Yassine • 10 • updated 6 weeks ago by Biostar ♦♦ 20
3
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2
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197
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2
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Stringtie: use htseq-count or prepDE.py to extract reads?
stringtie deseq2 rna-seq edger written 7 weeks ago by heyang • 0 • updated 7 weeks ago by ATpoint ♦ 18k
0
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166
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0
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Identify jumbled transcripts (scrambled exons) using HISAT2, stringtie, and GFFcompare?
stringtie rna-seq gffcompare hisat2 written 8 weeks ago by wolfgang.rumpf • 10 • updated 8 weeks ago by danbileedg2019 • 0
1
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0
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202
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0
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Isoform level differential expression
stringtie ballgown rna-seq written 9 weeks ago by rnaseql • 0
4
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2
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169
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2
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StringTie strandness of library in dUTP protocol
rnaseq libraryprep stringtie dutp written 10 weeks ago by raquelgarza95 • 40 • updated 10 weeks ago by Juke-34 • 2.2k
1
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1
answer
172
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1
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Warning: gene "NR_111945" (on chr1) has reference transcripts on both strands?
stringtie rna-seq written 12 weeks ago by swarajgaikwad15 • 0 • updated 12 weeks ago by Devon Ryan ♦ 90k
0
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0
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247
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0
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hisat2-stringtie-ballgown pipeline gives high p-value and q-value for RNA-seq of Arabidopsis thaliana
ballgown arabidopsis stringtie rna-seq hisat2 written 3 months ago by tiancaigg • 0
0
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0
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189
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0
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getting the test results of multiple transcripts; even though, I am using gene-level analysis
stringtie rna-seq written 3 months ago by Fawzi Yassine • 10
0
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0
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1.7k
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0
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Warning: no reference transcripts were found when map the reads to reference sequences by using stringtie
stringtie rna-seq written 21 months ago by Yuyin110 • 10 • updated 3 months ago by Kanoo • 0
0
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0
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284
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0
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ballgown error: Error in file(file, "rt") : invalid 'description' argument Calls: ballgown -> read.table -> file
ballgown stringtie rna-seq written 3 months ago by RNAseqer • 110
0
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1
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258
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1
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Problems with the reference genome in Stringtie
stringtie reference genome rna-seq lncrna written 3 months ago by iraia.munoa • 60 • updated 3 months ago by Devon Ryan ♦ 90k
6
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1
answer
217
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1
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Too low FPKM values from StringTie
new tuxedo stringtie rna-seq written 4 months ago by SJ Basu • 30
4
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2
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385
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2
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Stringtie elimination of important transcripts
assembly stringtie alignment rna-seq hisat2 written 5 months ago by ra2967 • 10
0
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1
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481
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1
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How to map RNA-seq with hisat2, stringtie, an assembly fasta, a gtf file, and a transcript fasta?
stringtie hisat2 mapping transcriptome written 5 months ago by O.rka • 110 • updated 5 months ago by swbarnes2 ♦ 5.8k
1
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1
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288
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1
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StringTie - Multimapped reads
assembly stringtie rna-seq multi-mapped reads written 5 months ago by sneha108.ss • 0 • updated 5 months ago by kristoffer.vittingseerup • 1.8k
2
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2
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1.9k
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8 follow
2
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Regarding getting gene count tables for DeSeq from StringTie using prepDE.py
stringtie rna-seq written 22 months ago by pixie@bioinfo • 1.4k • updated 5 months ago by kashifahmad750 • 0
1
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1
answer
239
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1
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Add double qoutes around transcript_id in gtf file
gtf stringtie rna-seq awk written 5 months ago by BioBaby • 0 • updated 5 months ago by finswimmer ♦ 11k
2
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1
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432
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1
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What's the difference of FPKM generated by htseq and stringtie?
htseq fpkm stringtie written 6 months ago by hxlei613 • 80 • updated 6 months ago by Devon Ryan ♦ 90k
0
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0
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242
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0
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Expression data from cufflinks merged gtf
bedtools gtf stringtie rna-seq written 6 months ago by ddowlin • 70
0
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1
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300
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1
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'gene_name' is missing in StringTie output file 't_data.ctab'
stringtie deseq2 new tuxedo protocol rna-seq written 6 months ago by swarajgaikwad15 • 0 • updated 6 months ago by Viswanathan • 0
0
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1
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367
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1
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Hisat2 output for stringtie
stringtie hisat2 written 6 months ago by Sam • 110 • updated 6 months ago by Vijay Lakhujani ♦ 4.1k
0
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1
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457
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1
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Error in running DESeqDataSetFromTximport
tximport R stringtie deseq2 rna-seq written 7 months ago by ankur • 0 • updated 7 months ago by Devon Ryan ♦ 90k
2
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1
answer
357
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1
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Unable to create file for tximport
tximport stringtie deseq2 rna-seq written 7 months ago by ankur • 0 • updated 7 months ago by kristoffer.vittingseerup • 1.8k
3
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2
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356
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2
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How to compare kallisto and stringtie output
stringtie next-gen kallisto rna-seq sequencing written 7 months ago by yusuf • 0 • updated 7 months ago by kristoffer.vittingseerup • 1.8k
4
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0
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447
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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 7 months ago by swarajgaikwad15 • 0 • updated 7 months ago by WouterDeCoster ♦ 39k
0
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1
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385
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1
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Where to find a valid GTF file for stringtie asssembly?
gtf stringtie transcriptome written 8 months ago by Vijay Lakhujani ♦ 4.1k • updated 8 months ago by Damian Kao ♦ 15k
2
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1
answer
626
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1
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stringtie merge error bam file not sorted
stringtie rna-seq written 8 months ago by paumarc • 10
1
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1
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936
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1
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Gffread error: Error (GFaSeqGet): subsequence cannot be larger than...
stringtie gffread rna-seq written 23 months ago by jjrin • 10 • updated 8 months ago by spriyar • 10
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