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• Problems with understanding cufflinks output
  Good evening, I did Cufflinks correspnding to an annotated genome. I want to download transcrip...
• chimeric transcripts detection tool
  Hi, How many tools can one find in the galaxy local too shed for detection of chimeric/fusion tr...
• 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...
• Problem In Manage Data Library
  We have found that, in Galaxy, when we add dataset to a library under Manage data libraries, Gala...
• Galaxy Doesn'T Detect The File When We Add Dataset To A Library Under Manage Data Libraries
  Hi list, We have found that, in Galaxy, when we add dataset to a library under Manage data libra...
• 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...
• Cufflinks Set Parameters
  Hi,   It's the first time for me to use cufflinks in galaxy, two choices confused me as follows: ...
• Strand Specificity
  Dear All, I am trying to analyze my RNAseq data by TopHat-Cufflinks package based on Galaxy. I u...
• 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...
• regarding gff3 file for rna seq analysis (tuxedo workflow) in human
  I want to analyze the rna seq data using tuxedo work flow. i have two replicates for control and ...
• Transcript sequence from Cufflink information
  Good evening I have successfully used TopHat and Cufflinks. I have selected a single annotated ...
• Snp And Indel Detection
  Hello, I am new using Galaxy, I would like ask if it is possible to perform a SNP and INDEL anal...
• Rna-Sea analysis and cufflinks
  Hello, I am using the following pipeline to analyze my RNA-Seq data to detect differences in gen...
• regarding to mapping and ontology
  Hello, I am done with BLASTX against NR and Swiss-Prot database with my non-model plan...
• Different RNA-seq result when I look at the gene_differential file and the transcript_differential file generated by cuff-diff
  Hi, I am wondering what is the exact difference between the gene list of the **transcript differ...
• Variant calling query with Unified Genotyper (deprecated GATK tool)
  Hi, I am trying to do exome analysis for Single Nucleotide variants detection. I have a doubt on...
• Gene Fusion Detection Workflow
  Hi - Has anyone developed a gene fusion detection workflow in Galaxy that they would care to share?
• Cufflinks Related Problem
  Dear Noa, Can you please tell me the parameters that I should keep while mapping bacterial tran...