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• Denovo transcriptome assembly
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• Intron finder for 3' UTR sequences (non-model organism)?
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• merged transcripts from RNA de novo assembly to create a reference transcriptome
  Hello, I have created de novo assemblies from RNAseq reads using velvet/oases for different subj...
• Merge 2 de novo assembly generated using Trinity?
  Hi Fellow Users, In past I have generated transcriptome de novo assembly for plant using trinity...
• COG annotation server for Assembled transcriptome data?
  Dear All, Is there any web servers, tools to annotate the assembled transcript(.fasta) file to g...
• Determining Fpkm Of De Novo Assembly Of Transcriptome
  I've done a de novo assembly of RNA seq data, but now want to determine the FPKM of each transcri...
• Intron/Exon structure by cDNA SRA file
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• Merging multiple sets of transcripts (generated by Trinity)
  Hi everyone. Need your advice on an issue I'm having. So, I have used Trinity in order to creat...
• gffcompare class code 'j'
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• How to get --transcript-to-gene-map <file> in RSEM?
  Hi dear one, In reference building step in RSEM, there is an option "**--transcript-to-gene-map ...
• Finding Novel Transcripts From A De Novo Transcriptome Assembly
  I've assembled a de novo transcriptome from RNAseq data. I'm comparing it against a reference cDN...
• Differential gene expression from RNAseq data. Before or after annotation?
  Hello community, I have this doubt and I have read different versions. However, most of them are...
• Gene expression level with RNA-seq
  Hello all, I want to ask a basic question because this is the first time I try RNA-seq analysis....
• Cufflinks de novo assembly, single transcript per gene
  I'm attempting to perform de novo transcriptome assembly using cufflinks. I have a single aligned...
• Stringtie/Cufflinks with yeast RNAseq
  Hi Biostars, I am working with yeast RNAseq data, and want to do guided transcriptome assembly u...
• which sequence file should be transcripts in full-length transcriptome analysis
  Hi, I haven't analysis Pacbio sequence data before. Now, I have some results form pacbio full-le...
• How to map RNA-seq with hisat2, stringtie, an assembly fasta, a gtf file, and a transcript fasta?
  I have the following files: assembly.fa transcripts.fa annotation.gtf My organism is eukaryotic ...
• Transcriptome assembly to validate annotations
  Hi everyone, Several gene annotations have been made on the fungal species I'm working on. I wo...
• How To Modify A Reference Based Transcriptome Assembly?
  I am interested in Reference based transcriptome assembly for my species of interest for which th...
• Is transcriptome assembly a necessary step in RNA-seq?
  In my RNA-seq analysis, I use hisat2 to map my clean RNA-seq reads to the genome. Then, I use Fea...