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• analyse the data form the CCLE(cghub)
  Hi I download the a RNA seq data(Aligned) from the cghub browser. The format of the file is the...
• Chip-Seq, Encode Peaks And Galaxy
  Hi everyone, I have a list of genomic regions with some variants and would like to study the cor...
• Excluding promoter and exon peaks
  Hi, would appreciate if someone could advise me on how to exclude promoter and exon peaks after p...
• Sequences Are Not Currently Available For The Specified Build
  Hi all, We are just beginning to analyze RNA-seq data and hope to make use of the Galaxy tools. W...
• Human RNA-Seq paired-end libraries
  Hello, I would like to study and doing exersizes in RNA-seq analysis that are based on paired-en...
• EBI SRA Data Import
  Hi guys i have just imported these datasets into Galaxy in fastq format http://www.ncbi.nlm.nih...
• Editing reference genome for TopHat on Trapline
  I am trying to use the Trapline workflow for RNA-Seq data, and have read the manual. I want to ed...
• intron retention analysis
  Hi! I am hoping to use the analysis tools that are available in Galaxy to achieve my tasks. I am ...
• FIle transfer from GEO to usegalaxy.org
  I'm trying to import some public GEO data into usegalaxy.org - specifically, the mouse RNA-seq da...
• cufdiff output-cutoff pvalue and parameters for differential expression
  dear all i am analysing rna seq data using galaxy pipeline for differntial expression. i have run...
• Parallel Processing Of Multiple Files On A Multi-Processor Box?
  Hi, I have an RNA-seq study with 6 runs. The output is 6 Illumina fastq files. I would like to...
• Generate SQ Lite database for cummeRbund not working with CuffDiff, and other general questions
  Hi everyone, I am currently a final year undergraduate studying at UoM set with the final yet pr...
• How to study just one stretch of a certain chromosome for transcribed RNAs.
  Hi all, I am new to Galaxy. How can I study just one stretch of a certain chromosome for transcr...
• studying a locus for different variants of an expressed lnc-RNA
  I have done FASTQ groomer, Tophat and cufflinks on FASTQ data. Now, I want to study a pre-defined...
• virome data analysis
  I want to know how to analysis virome data for viral metagenome study from de novo assembled blas...
• SAMtools Merge BAM files hangs
  Hi all, I am using TopHat to map RNA-seq reads. My study species is a non-model organism, so I c...
• Cufflinks Reporting Fpkm Values Of All Zeroes (0)
  Hello! I have come across a problem where Cufflinks is reporting all FPKM values ...
• error no 104
  Hi, I am unable to upload dataset from the study PRJNA176451 to my galaxy account. I encounter e...
• Inquiry On Fastqc Report
  Dear Galaxy Officer, Good day. I am a new user of Galaxy main server. The tools provided are ve...
• How can I improve my mapping alignment rate with MiSeq 2x300 bp paired-end reads?
  Edit 1: it appears I have misinterpreted the raw data, which in turn led to my poor results. The ...