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• Tool problems when using older versions of downsampled tutorial data
  Hi, I'm a newbie in Ref-seq and I'm trying to make a pipeline using HiSat -> HtSeq -> DESeq...
• Multiple FASTQ files per replicate
  Hi There, I'm running an RNA-seq analysis using FASTQ data from an Illumina HiSeq Rapid V2 machi...
• Correct way to do comparisons with DESeq2
  I have a RNA-seq experiment with paired-end reads from 6 samples. Each sample is a different geno...
• RNA Seq workflow with dataset collections
  Hi, I am trying to code a simple rna seq workflow that will use dataset collections. I want to ...
• Combining Reads from 2 Lanes
  Hi, I'm running an RNA-seq analysis to look for differentially expressed genes. I'm using sing-e...
• Output normalized RNA-seq data from DESeq2
  Hello- Is it possible to out put the normalized data from RNA-seq DEXSeq2 analysis? I don't see ...
• Header on Deseq2 result files
  I am using Deseq2 on galaxy for RNA-Seq data analysis. Earlier when I used to do differential exp...
• Cuffdiff No isoform FPKM Tracking and differential testing
  Hi All,  my dataset is an RNA-Seq set from illumina; workflow includes Tophat for Illumina ->...
• RNA seq beginner
  I just got back RNA seq data produced on the HiSeq 4000. They prepared the libraries and performe...
• what is a "Tabular file with Transcript - Gene mapping" in DESeq2?
  I have RNA Seq data from two conditions using a non-model organism. I constructed a trinity assem...
• Cuffcompare Or Cuffmerge
  Hi all, I read one paper "Differential gene and transcript expression analysis of RNA-seq experim...
• Cufflinks/merge/diff tools deprecated
  I've been using a HISAT2 -> Cufflinks -> Cuffmerge -> Cuffdiff -> CummeRbund pipeline...
• Deseq2 usage Galaxy
  Hello, I am trying to do some differential expression count on RNA Seq data using Galaxy. I did a...
• Cuffdiff 2.2.1.5 error with cummeRbund SQlite. "Fatal error: Exit code 1 () -- use version 2.2.1.3 instead
  Hi, so as a disclaimer, I am very new to RNA seq analysis. I received the following error while r...
• Making a Temporary Directory in an XML File
  Hi all. I'm making a custom bowtie tool, because the current bowtie tool only accepts FASTQ files...
• Rna-Seq Mutation Detection
  Hi,   I am trying to look at differences between two RNA-seq samples to see if there are mutation...
• Converting transcript data from Salmon to gene level TPM
  I have got TPM data from running Salmon on RNA-seq data. However, this is TPM for each individual...
• DESeq2 Fit Type Choice
  Hey folks, I am assessing results of gene-level differential expression testing with DESeq2, and...
• Galaxy For Gene Expression Comparison
  Hello, I am comparing RNA expression in two groups of rats, a drug treated group against a cont...