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• What galaxy tool should I use to compare these regions?
  What galaxy tool should I use to compare CTSS (CAGE-detected transcription start sites) regions w...
• Regarding Fusion Transcript Detection
  Hi, Is there no tool in Galaxy which can detect chimera transcripts ??? warm regards, Amit
• Mapping short sequences to each transcript for a given gene
  Hi Folks Ap;ogies up front for a newbie question. I have a set of short gene targeting sequence s...
• Cufflinks assembles very small number of transcripts from RNA-seq data
  I mapped RNA-seq data to reference genome and tried to assemble transcripts using cufflinks.It is...
• difference between MPileup multi-way pileup of variants and Generate pileup from BAM dataset
  hello everobody , in my project , i have to detect the variants (SNP and indels) in my genome se...
• Problems with MACS peak calling--FDRs of 100%
  Hello, I am having some issues with MACS peak calling. I have 5 files in my ChIP-Seq dataset (in...
• Chimeric Reads Detection
  hello, I am a beginner Galaxy user and I need to perform chimeric sequences detection on single ...
• Beginner question: Finding the right tool
  I'm a complete beginner at using Galaxy, and was hoping that someone could help me find the right...
• Locally cached sequence not detected from DBkey in cuffmerge when using mm10
  Hi, I'm running a cufflinks pipeline on the public server, and I'm having trouble using the loca...
• Problems with understanding cufflinks output
  Good evening, I did Cufflinks correspnding to an annotated genome. I want to download transcrip...
• How to classify the variants into different groups?
  Hello, This is my first time using galaxy. I ran Free Bayes to detect the variants of a data set ...
• Galaxy Tuxedo Protocol Questions
  Hi everybody, I'm totally new to RNA-seq analyses and it's my first time doing this and using Ga...
• 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...
• Rna-Sea analysis and cufflinks
  Hello, I am using the following pipeline to analyze my RNA-Seq data to detect differences in gen...
• A question of concept?
  Hi all! I'm new to this so, pardon my noobness. If I were to convert the transcript annotations...
• Trimmomatic data detection
  Hello I have a problem by detection data sequences uploaded in format fastqsanger by Tools/NGS :...
• Extract Spliced Transcripts From Cuffmerge
  Hi All, I have mapped RNA-Seq reads to an unannotated partial genome assembly and assembled them...