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• Strand Specificity
  Dear All, I am trying to analyze my RNAseq data by TopHat-Cufflinks package based on Galaxy. I u...
• 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 ...
• Naive Variant Caller
  I am using RNA-seq data for two different species and their hybrids. I want to find all positions...
• Performing Operations On Tab Delimited Text Files
  Hi, My name is Lanelle Edwards. I am a new galaxy user. I uploaded a tab delimited text file to m...
• Performing Operations On Tab Delimited Text Files
  Hi, My name is Lanelle Edwards. I am a new galaxy user. I uploaded a tab delimited text file to m...
• mapping over lapping genes to CNV probes
  I am very new to galaxy. I have CNV call data which has a start position and stop position for th...
• filtering pair-end bam file
  Hello, I am trying to filter a pairend bam file to get only forward reads in Galaxy. A bam filter...
• HISAT seems to assign wrong XS tag value to some reads of stranded RNAseq data
  Hi All, I have some paired end stranded RNAseq data prepared using an Illumina TruSeq Stranded m...
• Question: Problems with Filter pileup when performing Heteroplasmy tutorial
  Hello Galaxy, I am trying to do the Heteroplasmy tutorial from the tutorial page so that I can u...
• Fetch Alignments using Stitch Gene blocks, but '-' strand has been joined wrong
        As I use Fetch Alignments => Stitch Gene blocks extract genes from the maf file accordin...
• sort reads by start position
  I did RNA sequencing and many reads map to tRNA regions. Specific tRNAs are completely covered b...
• Trying to understand the steps for 'identify DNA polymorphism sites'
  Greetings! My partners and I got this homework. We're not specialized in bioinformatics or anythi...
• How to interpret and control for effects of primer contamination?
  Hi all, I'm currently analysing some RNAseq samples which were amplified prior to library prep an...
• how to determine direction of transcription of PE 100bp RNAseq
  Hi, We have performed 100bp PE RNAseq with libraries prepared with the Illumina Truseq stranded ...
• Filtering BAM files from HISAT2
  Hi. I am new to rna-seq and I have a couple of quick questions. My input was paired-end non-stran...
• 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) ...
• VCFFilter tool update from version 1.0.0 to 0.0.3
  I want to add VCFFilter 0.0.3 in Galaxy Tools, how do I do that...Please help. Currently the ve...
• Re: Assemble A Consensus Genome From Ngs Data
  Hi David, I'm sorry for a slow response. Relatively recently I solved a problem a bit like this a...