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• Same Rnaseq Samples Give Different Fpkm Values When Run Against Different Samples
  Hello, I am sure this has come up before and maybe I missed the answer. If in using cuffdiff I r...
• Cuffdiff Values Different For Same Sample
  Hello forum, I have ran cuffdiff with two samples, treated vs untreated, and had certain values a...
• Macs2 running to one sample
  Good morning, Im working with samples from ChIP-seq, and now i'm using macs2, however when i use...
• Remove batch effects with galaxy
  Hello, I am having a problem with batch effects on my RNA sequencing data, where I try to determ...
• Bowtie2 samples are not queueing
  Hello, I ran bowtie2 last week June 16th 2017 and two of my samples have had trouble running thr...
• Analysis of forward and reverse reads
  Hello. Newbie here: I have recently done some chip-seq, and for each sample, I have different ...
• calculating Unifrac significance with more than 10 samples
  The max number of samples (categories) that can be used in the Unifrac Significance tool is 10 si...
• CuffDiff and normalization between runs
  Dear All! I am currently conducting an RNA-Seq experiment in which i have several samples (1 nor...
• Matched patient samples in Deseq2
  Hi, I wish to use the Deseq2 tool on Galaxy but I am unsure how to incorporate the fact that my ...
• Any Thing Wrong With My Cufflink Process In Galaxy?
  Dear all: Recently, I run cufflink in galaxy on the internet. I want to compare two samples, How...
• Cuffdiff With Three Groups
  Dear all, I ran Cuffdiff with 3 groups: A, B, C each with 2, 5 and 1 replicates respectively. Whe...
• 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...
• tophat running since 4 days
  Hi,   I am running my samples on galaxy.org and the tophat is running since 4 days kindly advis...
• comparisson of RNA-seq FPKMs across samples
  Dear BioStars community, I am trying to "recycle" some RNA-seq data published as supplementary m...
• Creating a Workflow for Variant Detection for 200 samples
  I have posted this question before and did not receive any responses. Let me try to articulate th...
• 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...
• DESEQ2 is not normalizing HTSEQ counts for some samples
  I have RNAseq HTSEQ count data for 3 individuals collected at 3 time points. I would like to perf...
• How do I reorder files in history?
  Dear all, I have uploaded many raw data files for 10 samples (8 files per sample). However, uplo...
• ChIP Seq Upload
  Hello, We uploaded some samples yesterday. So far 4 of the 6 samples have been loaded but the la...
• ITS amplicon fungal
  I have sequence of ITS amplicon of fungal's sample. how can i analyze them? what kind galaxy's t...
• Cufflinks output empty
  Hi, I am encountering a problem similar to that mentioned here: https://www.biostars.org/p/45848...
• Bowtie2 samples still in queue after 48 hours
  Hello, I am currently using Bowtie2 and my samples. 5 out of the 6 ran but one has been in the q...
• Each sample as a condition? - cuffdiff
  Hello everyone, I've been having doubts about running each sample as a condition to get the FPKM...