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  Hi, I just started to use galaxy to analyze our NGS data, so I'm not good at it. My purpose is t...
• quantifying differential gene expression across three groups using cuffdiff
  Hello, I am trying to identify differentially expressed genes across three groups.  The groups c...
• hg38 GFF3/GTF source
  Hi, I am trying to use cuffdiff to compare relative gene expression from some human cell line sa...
• 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...
• HISAT2 incompatible with CuffDiff ?
  Hey I'm trying to compare the transcript expression levels between two conditions. I have put ...
• RNA-Seq analysis for 2 genes
  Hi, I did RNA-seq for 20 samples and I am interested in the differential expression of normal tra...
• cummerbund tool error
  Hello, I recently tried differential gene expression analysis using an established workflow. I h...
• Using different reference genome yields different results in RNA-seq data analysis
  Hello, I've got some questions with my RNA-seq results generated by galaxy.  For the experiment,...
• Cufflink Workflow
  Hi, I want to compare gene deferentially expressed in two conditions (1 and 2). I don't have a GT...
• Gene expession in RNA-seq data from SRA
  Hi! I would like to check the expression of my gene of interest in expression data loaded fro SRA...
• Comparing FPKM Values Between 2 Cufflinks Outputs
  Hello, apologies if this is a dumb question, I am relatively new to RNAseq. I have processed 9 sa...
• Issues with Using CuffDiff Tool in Galaxy
  Hi,   I am analyzing microRNASeq data. My pipeline is qc reads, bowtie for alignment, cufflinks...
• Tophat somehow makes Cufflinks lose ribosomal RNA
  Hello, I am mapping yeast RNA seq data (ribozero) using Tophat followed by Cufflinks, Cuffcompar...
• Cuffdif Output Notest
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• How to get rid of the linker of the miRNA raw data?
  How to get rid of the linker of the miRNA raw data? I want to use the raw data, but I don’t  know...
• Controlling for batch effects in RNA-Seq data
  Hi, I was hoping that someone might be able to give me some advice on adjusting or controlling f...
• Error in CuffDiff
  I would be forever grateful if someone could take the time to help me. I am attempting to analyze...
• select line including special content and the following row as well
  I am beginner using galaxy. I would like to assort my fasta dataset about mature miRNA from mirba...
• Exceptionally High Rpkm Values Of Mirna And Other Short Genes In Cuffdiff'S Output
  Hi all, I have been analyzing my RNA-seq data on mouse tissues. My RNA-data is single-ended and 5...
• miRNA sequencing alignment
  i have a rna-seq data and would like to align it against micro RNA human. Can I do it in galaxy. ...
• Multiple FASTQ files per replicate
  Hi There, I'm running an RNA-seq analysis using FASTQ data from an Illumina HiSeq Rapid V2 machi...
• How Should I Include Biological Replicates In Cufflink/Cuffdiff?
  Dear team, I have a few questions regarding RNA-seq data analysis. I want to compare transcripto...
• Questions On Cuffdiff Output And Browser Visualization
  I would really appreciate someone's input on some issues I am having with my cuffdiff output for ...
• count and compare microRNA expression value in RNA-Seq data on Galaxy
  Hello, I have a question, I want to count and compare specific microRNA expression value in BAM ...