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5
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1
answer
86
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1
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StringTie "missing header error" [for both HISAT2 and STAR alignment files]
stringtie alignment tool rna-seq written 1 day ago by EagleEye • 4.7k
1
vote
2
answers
295
views
2
answers
How to extract fasta sequences from assembled transcripts generated by Stringtie
fasta gtf file stringtie sequences written 4 months ago by seta • 920 • updated 2 days ago by Vijay Lakhujani • 1.2k
3
votes
1
answer
193
views
1
answer
hisat2 parameters for paired end and single end reads from same samples
hisat stringtie alignment rna-seq hisat2 written 10 days ago by bioinfo17 • 10 • updated 8 days ago by Macspider • 1.5k
0
votes
0
answers
96
views
0
answers
Warning: no reference transcripts were found when map the reads to reference sequences by using stringtie
stringtie rna-seq written 11 days ago by Yuyin110 • 10
2
votes
1
answer
134
views
1
answer
Are TPM values generated by different programs comparable?
stringtie tpm kallisto written 23 days ago by amy.bashir • 50 • updated 23 days ago by h.mon ♦ 8.7k
0
votes
1
answer
201
views
1
answer
Regarding getting gene count tables for DeSeq from StringTie using prepDE.py
stringtie rna-seq written 28 days ago by pixie@bioinfo • 1.1k • updated 25 days ago by Satyajeet Khare • 1.0k
1
vote
1
answer
248
views
1
answer
Some basic question on quantification of RNA-seq mapped reads
alignment stringtie quantification rna-seq hisat written 6 weeks ago by Hamid • 10
0
votes
1
answer
256
views
1
answer
RNA-Seq : merged.gtf file from cuffmerge where exons are duplicated (two exons with the same coordinates and the same gene_id but without the same oId)
assembly stringtie rna-seq cuffmerge merged.gtf written 8 weeks ago by JoannaF • 0 • updated 8 weeks ago by Satyajeet Khare • 1.0k
2
votes
1
answer
193
views
1
answer
gffread error when extracting transcript sequences from gtf, coordinates exceed sequence length
rnaseq stringtie cufflinks gffread transcript written 8 weeks ago by jjrin • 10 • updated 8 weeks ago by victor.gambarini • 20
0
votes
0
answers
155
views
0
answers
Calculating the gene coverage in StringTie
gene stringtie coverage rna-seq written 9 weeks ago by sjbasu • 0
0
votes
0
answers
158
views
0
answers
Gffread error: Error (GFaSeqGet): subsequence cannot be larger than...
stringtie gffread rna-seq written 11 weeks ago by jjrin • 10 • updated 10 weeks ago by Biostar ♦♦ 20
3
votes
1
answer
391
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5 follow
1
answer
Using StringTie with DESeq2(StringTie geneID and corresponding Ensembl geneID)
stringtie deseq2 written 11 weeks ago by Megan • 30 • updated 11 weeks ago by stephensmithgalway • 20
0
votes
0
answers
172
views
0
answers
STAR/StringTie compatibility on tag HI in the BAM alignment file
stringtie star written 11 weeks ago by Megan • 30
1
vote
0
answers
202
views
0
answers
Help analysing StringTie output on Galaxy
stringtie galaxy rna-seq transcript assembly written 11 weeks ago by florian.laforets • 0
3
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0
answers
251
views
0
answers
Help regarding RNA-seq STRINGTIE pipeline and output
stringtie rna-seq written 3 months ago by pixie@bioinfo • 1.1k
0
votes
0
answers
204
views
0
answers
stringtie (.gtf) vs ballgown (t_data.ctab) FPKM values do not match - why?
stringtie ballgown fpkm rna-seq written 3 months ago by cpak1981 • 30
0
votes
0
answers
177
views
0
answers
StringTie -e estimate parameter
gene annotation stringtie rna-seq transcripts written 3 months ago by k.mooo • 0
0
votes
1
answer
250
views
1
answer
StringTie reports 0 coverage for all reference transcripts
stringtie rna-seq written 4 months ago by PoGibas ♦ 4.7k • updated 3 months ago by k.mooo • 0
0
votes
0
answers
273
views
0
answers
stringtie GFF Error: overlapping duplicate transcript feature
stringtie error written 4 months ago by 1374906590 • 0 • updated 4 months ago by genomax ♦ 33k
3
votes
1
answer
328
views
1
answer
Merging stringtie assemblies using stringtie merge
assembly stringtie merge rna-seq transcriptome written 5 months ago by Vijay Lakhujani • 1.2k
0
votes
0
answers
422
views
0
answers
Warning encountered while transcript abundance estimation using stringtie
stringtie rna-seq abundance written 5 months ago by Vijay Lakhujani • 1.2k
1
vote
1
answer
311
views
1
answer
Error running gffcompare
gff stringtie gffcompare rna-seq written 5 months ago by Vijay Lakhujani • 1.2k • updated 5 months ago by Macspider • 1.5k
0
votes
0
answers
290
views
0
answers
Cuffcompare on the merged GTF file produced by Stringtie
stringtie cufflinks cuffdiff splicing written 5 months ago by seta • 920 • updated 5 months ago by Biostar ♦♦ 20
0
votes
1
answer
253
views
1
answer
Error using StringTie
exit code 139 stringtie written 5 months ago by dabs17 • 0 • updated 5 months ago by Devon Ryan ♦ 70k
0
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2
answers
667
views
2
answers
Please adivse me on differential expression analysis on the STAR/Stringtie output
count stringtie star differential expression edger written 7 months ago by seta • 920 • updated 6 months ago by dunhamcg • 0
0
votes
1
answer
559
views
1
answer
An odd error with StringTie!!
rnaseq stringtie error written 7 months ago by seta • 920 • updated 7 months ago by Devon Ryan ♦ 70k
2
votes
0
answers
650
views
0
answers
RNA seq analysis using STAR+StringTie
stringtie star rna-seq written 8 months ago by fatima • 0
7
votes
1
answer
385
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1
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Generate more splice variant from RNA-seq data
stringtie isoforms rna-seq alternative splicing written 8 months ago by nim.1111.ou • 10
1
vote
1
answer
374
views
1
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StringTie with Ensembl annotation: Fuzzy exon identification
ensembl stringtie annotation written 9 months ago by jonasmst • 280 • updated 9 months ago by Macspider • 1.5k
1
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1
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1.1k
views
1
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How to run HISAT2 / Stringtie / Ballgown analysis starting with gff file
gtf gff stringtie hisat2 written 9 months ago by al-ash • 0
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