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• Cuffdiff output redundant genes
  Hello, I am using the Galaxy tool Cuffdiff to analyze the RNA-seq data. But for the output file "...
• Help with interpreting RNA-seq output
  I am new to galaxy and have been trying to figure out how to align RNA-seq reads to a genome in o...
• Problem With Repeated Genes In Cuffdiff'S Output
  Hi all, I am working on RNA-seq using TopHat/Cufflink/Cuffdiff for differential gene expression a...
• Rna-Sea analysis and cufflinks
  Hello, I am using the following pipeline to analyze my RNA-Seq data to detect differences in gen...
• Cufflinks Assigning separate Cuff I.D. to gene that falls within location of known gene
  Hi, I am following the workflow for differential expression analysis using cuffdiff on galaxy as...
• cufdiff output-cutoff pvalue and parameters for differential expression
  dear all i am analysing rna seq data using galaxy pipeline for differntial expression. i have run...
• RNA seq analysis
  i have done RNA seq on S2 Drosophila cells and want to check differential expression. I have my d...
• A Question About Cuffdiff "Values"
  Hello: I am a Galaxy-naive molecular, developmental biologist studying repression/derepression of...
• EBI SRA Data Import
  Hi guys i have just imported these datasets into Galaxy in fastq format http://www.ncbi.nlm.nih...
• Different RNA-seq result when I look at the gene_differential file and the transcript_differential file generated by cuff-diff
  Hi, I am wondering what is the exact difference between the gene list of the **transcript differ...
• Error with Cuffdiff
  Hi, I have used cuffdiff on my cuffmerge results. Then an error occurred. Could anyone tell me w...
• DE analysis of miRNA after mapping with miRDeep2 quantifier
  After small RNA sequencing I performed adapter, quality, and length trimming on fastq files. I th...
• Naive Variant Caller
  I am using RNA-seq data for two different species and their hybrids. I want to find all positions...
• Identifying Genes
  I am very new to Galaxy. We have performed a comparative analysis between the transcriptomes of d...
• Suggestion To Change Cuffdiff -C "Min Alignment Count" Default To Author'S Value Of '10'
  Hi Galaxy Developers, This is regarding the wrapper for cuffdiff and the -c parameter for "Min...
• Extract gene sequence from BAM.
  Hi, I have several BAM files with different samples of a chromosome and I want to end up with one...
• Differential Expression in bacteria RNA-seq
  Hello, I got a problem in Cufflinks: I need to analyze fastq file from a RNA-seq (I got bacteria...
• Chip-Seq, Encode Peaks And Galaxy
  Hi everyone, I have a list of genomic regions with some variants and would like to study the cor...
• Inquiry On Fastqc Report
  Dear Galaxy Officer, Good day. I am a new user of Galaxy main server. The tools provided are ve...
• Batch conversion of ID to gene symbol
  I'm an old school molecular biologist who studies gene expression but is quite new to bio-computi...
• Human RNA-Seq paired-end libraries
  Hello, I would like to study and doing exersizes in RNA-seq analysis that are based on paired-en...