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• How to find exonic and intronic regions from a set of coordinates?
  Hey, could anyone please help me with it? I have few coordinates of different chromosomes. I want...
• Exon number ucsc or other
  Hello, I am wondering how can i find exon number using regions start-end for 100 exons at the...
• Alternative To Fpkm From Cufflinks
  Hi all, Is there any way to find out the number of reads aligning to a transcript rather than the...
• How to get intronic+exonic reads using Htseq withing galaxy
  Hi, Im usnig Htseq for counting and the feature type is set to exonic by default so I am assumin...
• RNAseq analysis for Bacterial genomes
  Hello, I am interested in using the tuxedo suit to analyze RNAseq data from the bacteria Strepto...
• Exon, Intron or Promoter?
  Hello, I need help you. I have a file of CHIP-SEQ data in BED format and i analyzed those data wi...
• Coding And Non Coding Exons
  Hi, I am very new to the UCSC browser, I want to find the number of coding and non coding exons ...
• New Tools Available On Galaxy
  New tools released to Galaxy Test at http://test.g2.bx.psu.edu. 1. Gene BED to Exon/Intron BED (...
• Chromosome Coordinates to Annotation
  Hello, If I have specific chromosome coordinates, how do I find out if this region is Exon or In...
• Cufflinks duplicate GFF ID error - best course of action?
  Hi, I have a question regarding the best way to handle genome annotations that include duplicate ...
• using mPileup to examine allelic imbalance in hybrids
  Hi, I have some RNA-seq data for two different species and their hybrids. I want to look at the ...
• A Question Regarding Sequence Retrieval
  Dear Galaxy, I have the results for the sequence retrieval for Insulator ...
• Strand Specificity
  Dear All, I am trying to analyze my RNAseq data by TopHat-Cufflinks package based on Galaxy. I u...
• Bed To Gff
  I am trying to use the galaxy "BED to GFF" function. The operation worked, but instead of giving...
• Inconsistent Sequences
  Can anyone help figure out the following problem? I am interested in the exon positions and sequ...
• End Position of an alignment in BWA
  Hi, Does someone know if there is a way in galaxy to add a column in a dataset (for example a BW...
• How to join to data-sets correctly?
  Hi, I'm having difficulty in joining to data-sets to find the number of repeats in coding exons i...
• Exons with the lowest snp density
  How do I find exons with the lowest density? I am trying to compare Exons in human chromosome 22 ...
• Question About Extract Intron Sequences From [Gtf File] + [Genome Fasta File]
  Dear Jen, I am not much of a Galaxy user yet. Some days ago I know something about Galaxy and fo...
• intron retention analysis
  Hi! I am hoping to use the analysis tools that are available in Galaxy to achieve my tasks. I am ...