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<prev • 92 results • page 1 of 4 • next >
3
votes
1
answer
81
views
1
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Too low FPKM values from StringTie
new tuxedo stringtie rna-seq written 4 days ago by SJ Basu • 30
3
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2
answers
176
views
2
answers
Stringtie elimination of important transcripts
assembly stringtie alignment rna-seq hisat2 written 4 weeks ago by ra2967 • 10
0
votes
1
answer
141
views
1
answer
How to map RNA-seq with hisat2, stringtie, an assembly fasta, a gtf file, and a transcript fasta?
stringtie hisat2 mapping transcriptome written 5 weeks ago by O.rka • 70 • updated 5 weeks ago by swbarnes2 ♦ 4.8k
1
vote
1
answer
111
views
1
answer
StringTie - Multimapped reads
assembly stringtie rna-seq multi-mapped reads written 5 weeks ago by sneha108.ss • 0 • updated 5 weeks ago by kristoffer.vittingseerup • 1.4k
2
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2
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1.6k
views
8 follow
2
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Regarding getting gene count tables for DeSeq from StringTie using prepDE.py
stringtie rna-seq written 18 months ago by pixie@bioinfo • 1.3k • updated 5 weeks ago by kashifahmad750 • 0
1
vote
1
answer
143
views
1
answer
Add double qoutes around transcript_id in gtf file
gtf stringtie rna-seq awk written 7 weeks ago by BioBaby • 0 • updated 7 weeks ago by finswimmer ♦ 9.8k
2
votes
1
answer
238
views
1
answer
What's the difference of FPKM generated by htseq and stringtie?
htseq fpkm stringtie written 11 weeks ago by hxlei613 • 80 • updated 11 weeks ago by Devon Ryan ♦ 88k
0
votes
0
answers
136
views
0
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Expression data from cufflinks merged gtf
bedtools gtf stringtie rna-seq written 11 weeks ago by ddowlin • 70
0
votes
1
answer
171
views
1
answer
'gene_name' is missing in StringTie output file 't_data.ctab'
stringtie deseq2 new tuxedo protocol rna-seq written 12 weeks ago by swarajgaikwad15 • 0 • updated 11 weeks ago by Viswanathan • 0
0
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1
answer
190
views
1
answer
Hisat2 output for stringtie
stringtie hisat2 written 12 weeks ago by Sam • 100 • updated 12 weeks ago by biokoala ♦ 3.6k
0
votes
1
answer
209
views
1
answer
Error in running DESeqDataSetFromTximport
tximport R stringtie deseq2 rna-seq written 12 weeks ago by ankur • 0 • updated 12 weeks ago by Devon Ryan ♦ 88k
2
votes
1
answer
211
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1
answer
Unable to create file for tximport
tximport stringtie deseq2 rna-seq written 12 weeks ago by ankur • 0 • updated 12 weeks ago by kristoffer.vittingseerup • 1.4k
3
votes
2
answers
206
views
2
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How to compare kallisto and stringtie output
stringtie next-gen kallisto rna-seq sequencing written 3 months ago by yusuf.zhc • 0 • updated 12 weeks ago by kristoffer.vittingseerup • 1.4k
4
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0
answers
264
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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 3 months ago by swarajgaikwad15 • 0 • updated 3 months ago by WouterDeCoster ♦ 36k
0
votes
1
answer
184
views
1
answer
Where to find a valid GTF file for stringtie asssembly?
gtf stringtie transcriptome written 4 months ago by biokoala ♦ 3.6k • updated 4 months ago by Damian Kao ♦ 15k
2
votes
1
answer
383
views
1
answer
stringtie merge error bam file not sorted
stringtie rna-seq written 4 months ago by paumarc • 10
1
vote
1
answer
761
views
1
answer
Gffread error: Error (GFaSeqGet): subsequence cannot be larger than...
stringtie gffread rna-seq written 19 months ago by jjrin • 10 • updated 4 months ago by spriyar • 10
1
vote
0
answers
203
views
0
answers
Too Many StringTie Genes
stringtie written 4 months ago by gtasource • 20
2
votes
1
answer
250
views
1
answer
RNA-seq samples along different time points, how to run Stringtie?
stringtie rna-seq time-point written 4 months ago by iraia.munoa • 50 • updated 4 months ago by grant.hovhannisyan • 1.4k
1
vote
1
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615
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1
answer
Estimating the abundance of the transcripts and genes using stringtie
stringtie rna-seq written 13 months ago by amy16 • 30 • updated 4 months ago by iraia.munoa • 50
2
votes
1
answer
215
views
1
answer
How to deal with single transcripts assigned to multiple genes?
stringtie rna-seq hisat2 written 4 months ago by antoinefelden • 20 • updated 4 months ago by RamRS ♦ 20k
2
votes
2
answers
281
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5 follow
2
answers
Proper design for DESeq2 and other RNAseq general questions
stringtie deseq2 rna-seq hisat2 written 4 months ago by Stef • 0 • updated 4 months ago by swbarnes2 ♦ 4.8k
2
votes
1
answer
432
views
1
answer
FPKM matrix after stringtie using ballgown
stringtie ballgown fpkm rna-seq written 5 months ago by Vasu • 300 • updated 5 months ago by Adrian Pelin • 2.2k
4
votes
0
answers
221
views
0
answers
StringTie giving different results - same dataset
rnaseq stringtie denovo transcript assembly written 6 months ago by raquelgarza95 • 10
0
votes
1
answer
286
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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 6 months ago by ever_wudi • 10
0
votes
0
answers
236
views
0
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Stringtie merge generates close duplicates of original transcripts
stringtie written 6 months ago by jammydodger123456 • 10
2
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0
answers
875
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0
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how to find novel genes and transcripts in gffcompare?
stringtie rna-seq gffcompare written 13 months ago by naveenkumarv40 • 20 • updated 7 months ago by geek_y ♦ 9.1k
0
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0
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233
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0
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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 7 months ago by tawares07 • 0
2
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0
answers
555
views
0
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Stringtie output gtf file only contains STRG transripts, no original annotations
stringtie written 8 months ago by jammydodger123456 • 10
1
vote
1
answer
409
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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 months ago by Farbod • 3.2k • updated 7 months ago by biokoala ♦ 3.6k
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