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• How to identify the contigs for each predicted cds sequences?
  Hi, I have an assembled genome (contigs) and it's cds & proteins predicted by Augustus. For m...
• determination of alternate splicing events from assembled transcripts
  hi all, I want to determine alternative splicing events for my assembled transcripts (i used st...
• From HISAT2 to cuffdiff?
  Hey, I have an issue of not getting any expression values for CDS following: HISAT2 (against hg1...
• De novo assembled transcript mapping to genome scaffold
  Hi, I did mapping of illumina raw reads to CDS transcripts and I extracted unmapped raw reads. ...
• Identifying polyA tail sequences for predicted novel transcripts using STAR/Cufflinks
  Is it possible to use STAR for extracting info on presence or absence of polyA tail sequences for...
• Get protein domain information from nucleotide sequence of assembled contigs?
  Dear Friends, I have a set of predicted ORFs/CDS. I want to see if there are protein domains ava...
• How to compare CDS gff with genome guided assembled gff
  I am working on plant species transcriptome. Its draft genome is known. We want to identify some ...
• choice of reference for transcriptome assembly
  Hello People, I have non-model plant transcriptome data that has to be assembled in reference ba...
• according to given gene sequence predict its putative regulators(transcription factors and so on)
  hello everyone! if i have a complete cds of a gene, according to this sequence can i predict its ...
• Denovo Transcriptome Assembly
  I have a question regarding the denovo assembly and transcripts that were obtained from the assem...
• Validate Novel Isoforms Generated By Cuffcompare
  When I compare the assembled transcripts with a reference annotation with cuffcompare, one of the...
• Appropriate number of reads for assembling novel transcripts with Trinity?
  I'd like to detect novel transcripts in a cancer sample with Trinity. I'm sequencing on an Illumi...
• need to identify CDS (translation) for gene models predicted by Cufflinks and Stringtie
  I have transcript models in GTF format made from assembling RNA-Seq read alignments using stringt...
• 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...
• minimum recommended length for transcript prediction -Stringtie
  Hi all, Can you please advise me on what is the minimum recommended length for transcript predict...
• Best Approach To Predict Novel And Alternative Splicing Events From Rna-Seq Data
  Hi All, I am looking for the best approach to predict novel and alternative splicing events from...
• Ucsc Browser And Novel Snps
  Hello Can the UCSC browser be used to predict the effect of novel SNPs on a transcript (e.g. syn...
• Cufflinks reports less transcripts then in gff
  Hi Biostars, To make transcriptome assembly, I mapped the reads (2x75, strand-specific, organism...
• Cufflinks On Chromosome 2
  Hello everyone, I have a sorted and index BAM file. I want to run cufflinks on just Chromosome2 ...
• Method to identify novel transcript based on strand-specific RNAseq
  Dear all, I have strand specific RNAseq data at hand, and aim to get novel transcripts being dif...