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• Problems with understanding cufflinks output
  Good evening, I did Cufflinks correspnding to an annotated genome. I want to download transcrip...
• Cuffdiff only giving gene names to certain sequences
  Hi everyone, I have been trying to figure this out for the better part of a week so hoping someo...
• Extract Sequences From [Gtf File] + [Genome Fasta File]
  Hi Galaxy people, I have transcripts predicted by Cufflinks that are in a gtf file. How can I ex...
• Cuffcompare Or Cuffmerge
  Hi all, I read one paper "Differential gene and transcript expression analysis of RNA-seq experim...
• Locally cached sequence not detected from DBkey in cuffmerge when using mm10
  Hi, I'm running a cufflinks pipeline on the public server, and I'm having trouble using the loca...
• Cuffdiff Tracking File Does Not Report All Genes And Trancrips From Reference Annotation?
  Hi, Galaxy user. I ran into a problem when using Cuffdiff 1.2.1 in Galaxy local instance to check...
• Extract Data And New Genes
  Hi Everyone, I am working with *Aedes aegypti * and I obtained around 500 million reads (HiSe...
• extracting sequence from E. coli genomic sequences
  In the lab I conjugated a bacteria of interest with E. coli and was able to transfer an antibioti...
• Mapping short sequences to each transcript for a given gene
  Hi Folks Ap;ogies up front for a newbie question. I have a set of short gene targeting sequence s...
• Rna-Seq Analysis
  Since the pictures are too big for the mailling list. I will upload it in seperate emails. Dear ...
• Cufflinks output files
  I have performed Cufflinks on a TopHat file and obtain the 5 files without any error message. Ho...
• Rna-Seq Analysis
  Dear all, I am using Galaxy for RNA-Seq analysis. I expect two lists: differentially expressed tr...
• Extract Genomic DNA tool behavior
  Hi I have downloaded RNA_seq data as fastq files and aligned these against FASTA sequences as re...
• Blank Cufflinks output
  Hi! I am conducting an RNA-seq analysis with Saccharomyces cerevisiae-derived data. In my workfl...
• htseq and cufflinks
  Hi, I have used HTSeq to count the no of mapped reads, the HTSeq gives me the ensemble ids but w...
• fasta generation for functional elements
  Hi,   I have got several suggestion how to extract fasta sequence from assembled cufflinks like...
• Cufflinks Gene Transcripts
  Hi I have been experimenting with Bowtie and Cufflinks and I now reach a point where it appears t...
• How to get gene sequences (DEGs) not transcripts sequences?
  Hello, my name is one of Galaxy user in Korea. I conducted cuffmerge -> cuffquant -> cuff...
• how to get fasta sequences of cufflink assembled transcripts
  hi i request you to help me in getting the fasta sequences of assembled transcripts by cufflink....
• Cufflink Workflow
  Hi, I want to compare gene deferentially expressed in two conditions (1 and 2). I don't have a GT...
• Difference between mRNA, CDS, transcript and gene in annotation file
  Hi, I am new to bioinformatics and have a very basic question. In the annotation files (gff) ava...