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• No ht-seq in main Galaxy menu?
  Why is there no way in the main Galaxy menu to produce a raw counts matrix (not normalized and no...
• voom normalized count data matrix (Differential count 0.3.0)
  Hi, I have used voom from the "Differential count" package and it worked smoothly. I would like t...
• Normalization of RNA-seq data
  Hi, I am wanting to normalize my RNA-seq data without running a differential gene expression on...
• Clustering With Cuffcompare Or Cuffdiff Results
  Dear Sir or Madam, I am planning to do clustering of several libraries based on the output of cu...
• Homer getDiffExpression.pl edgeR
  To complement out cuffdiff analysis we thought to take a parallel route using Homer. to do so we...
• Extracting Raw Count Data From Mapping
  Hi, I would like to extract raw counts from tophat output. Does anyone know a way to do this in...
• How to get raw reads from bam file
  Hi, I can't figure out how to get raw reads counts from a bam file. I have 3 different experimen...
• 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...
• Use multiple inputs in same script
  Hi all, I have a batch of 170 samples (represented by 170 comma-separated files) and am attempti...
• Read counts for limited genome regions
  Hello: I would like to get raw reads depth at each genome position for a limited region of the c...
• To merge several count data into one matrix.
  Hello all. I would like to merge or combine my count data into one matrix for using Degust prog...
• How to analyse the gene expression matrix which I downloaded from GEO by Galaxy?
  I downloaded the gene expression matrix from the GEO, it is excel format. In this file, there are...
• I am slightly confused about the input requirements for the differential expression tool - last step of Trinity
  Hello all, I have a pressing question... To start with, I have read the Trinity methods paper ...
• NGS Qc: MultiQC not recognizing FASTQC raw results from list
  Hi, I am trying to aggregate results from FAST Qc lists by MultiQC, but MUltiQC isnt recognizing...
• 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...
• raw data (23andme or Ancestry) free access for research
  Hello to all, I am doing genetic tests (AncestryDNA and 23andme) on me and my family and I will h...
• Critical Feedback
  This student was more adventurous. I think he actually could do more of what he tried with more e...
• multiplex primer design...Help!
  Hi I'm trying to design a suite of 10-15 microsat primers using NGS. I have the raw output files...
• Cuffquant errors after using HISAT2
  Hi, I have 2 sequence reads archive and I want to do some RNA-Seq analysis on them. Archive 1 :...
• Using DESeq w/ counts from different RNASeq experiments
  Hello there I have count files from 3 different sequencing experiments on similar samples but wi...
• 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 ...
• Internal Fail error 500 or file failed
  What am I doing wrong? My files have an extension of .fastq. I am told that these files contain r...