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• Tophat Mapping
  Hi, After mapping RNA-Seq paired end reads with Tophat, I can see that most of reads fall into...
• Stitch Gene Blocks From MAF for non-coding region
  Dear Galaxy, I am attempting to stitch alignments from 46MultiZ MAF for a non-coding transcript....
• Deseq2 transcript list classification
  Hi everybody, I did RNA-seq on mouse stem cells and i got a list of differentially expressed tran...
• 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 ...
• Synonymous And Non-Synonymous Snps
  Hi, I have been taking a look at Galaxy and playing with it a bit. I have also watched several o...
• Inconsistent Sequences
  Can anyone help figure out the following problem? I am interested in the exon positions and sequ...
• 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 (...
• Bed12 Format For Stitching Blocks Given A Set Of Coding Exon Intervals
  Hi Galaxy, I am trying to stitch together MAF alignments for the coding sequence for a few genes...
• How To Get A List Of Coding Exons In Which Each Exon Is Represented Once.
  Hey everyone, I am a new galaxy user. I am trying to upload coding exons of specific region from ...
• Constitutive Exon Workflow?
  Hi folks, I'm trying to find over the entire human genome, for each gene, which exons are the mos...
• Finding Constitutive Exons Using Expression Data
  Hi, I'm trying to find over the entire human genome, for each gene, which exons are the most cons...
• DEXseq count reads tool obtaining only zero counts for all exons
  I'd like to run DEXseq on my RNA-seq dataset to identify any potential differences in exon inclus...
• Finding Conserved Non Coding Region
  Hi all , I have a set of 1500 sequence obtained from my Chip_Seq experiment. I am interested to K...
• Alu elements positions
  Hi all, Could you help me to fined Alu elements in genes as a  part of their coding exons Regards
• Duplicate row names error with EdgeR on FeatureCounts files
  Hi all, I created tabular count files using FeatureCounts with a GTF file (iGenomes, UCSC hg38) ...
• Question about cow refference genome
  I would ask about which reference cow genome should I use for RNAseq data analysis in Galaxy to f...
• 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...
• Micro-RNA Host Genes
  Hi, I have carried out differential expression analysis using Deseq2. One of the most differentia...
• 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 ...
• Help!! Tophat Paired End Reads
  Hi, I am very confused by my mapping. Please help me figure out what's wrong with my operation. ...
• Exon number ucsc or other
  Hello, I am wondering how can i find exon number using regions start-end for 100 exons at the...
• Galaxy With Cuffdiff Output
  Dear all, I use cuffdiff in galaxy net version. The output are isoform.diff , gene.diff ...etc...