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• mRNA expression Count
  Hi, I want to get mRNA expression count from RNA-Seq data. I am able to get gene expression coun...
• RNA-Seq raw count data analysis using GALAXY
  Hi, I have downloaded the raw_readcounts files (.txt files) from an RNA-Seq experiment using GSE ...
• 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...
• Why shouldn't you ever compare TPM values across samples?
  There is a warning in red letters in galaxy manual: "You should NEVER EVER use RPKM, FPKM, or TP...
• Counts vs FPKM
  I was able to retrieve the counts from my RNAseq analysis via Cuffdiff so as to compare with the ...
• HTSEQ count error
  Hello, This is my first rna-seq data analysis project and I am using Galaxy to analyze different...
• Deseq2 usage Galaxy
  Hello, I am trying to do some differential expression count on RNA Seq data using Galaxy. I did a...
• DESeq2 Fit Type Choice
  Hey folks, I am assessing results of gene-level differential expression testing with DESeq2, and...
• Cuffdiff: Same Gene Listed With Different Fpkm Values
  Dear all, has anything like this happened to you? I compared two samples with cuffdiff and when ...
• TopHat aligning with ensembl in Galaxy
  I'm using the Galaxy interface to analyse RNAseq data. I've successfully aligned using the defaul...
• stringtie output from multiple samples into an FPKM matrix
  Hi all, Anyone have a good set of steps to take the stringtie transcript-level expression output...
• Can limma's voom take normalized counts as input?
  Hi,      I am currently analyzing some RNASeq data from TCGA - which is data that has been proce...
• RNAseq exon count
  Hej, I have an RNAseq dataset (single end) from a mouse model heterozygous for a trapped-gene. Th...
• Rna-Seq Analysis Withtout Reference Genome
  Hi all, I'm about to start doing gene expression analysis but i don't have a reference genome. I...
• Homer getDiffExpression.pl edgeR
  To complement out cuffdiff analysis we thought to take a parallel route using Homer. to do so we...
• comparisson of RNA-seq FPKMs across samples
  Dear BioStars community, I am trying to "recycle" some RNA-seq data published as supplementary m...
• Min Alignement Count
  Dear Galaxy team, I am performing a differential expression analysis with a cufflinks- cuffmerge...
• About rarefaction curve : FROGS pipeline
  Hello everyone, I am doing a metagenomic analysis on Galaxy with the pipeline FROGS. Everything ...
• Impossible to use Htseq-count on BAM files from Tophat2
  Hello, I'm currently facing troubles using galaxy. I want to compare differentially expressed ...
• ChIPseq vs RNAseq comparison
  Hello, I have a number of RNAseq bigwigs and ChIPseq bigwigs and would like to compare overall h...
• How do I obtain gene names from ENSG values?
  Hi I have performed DGE using DESEQ2 (input htseq-count, following mapping by BWA-MEM) and have ...