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• Galaxy cummeRbund fails to identify sample name for X and Y axis for scatter and volcano plot
  Hello, I have cuff diff sqlite db for 2 samples and I wish to visualise the result using galaxy-c...
• Problem with Plotting tool
  I need to make a rarefaction curve and i´m want to to this: Plotting tool with the followin...
• significant genes not shown in the scatter and volcano plots
  hello, When i plot the scatter plot and volcano plot for my cuffdiff output using cummeRbund it s...
• Overlapping axis labels when graphing quality score box plot
  Hello~ Small SOS. I'm trying to graph the quality box plot and the nucleotide distribution chart...
• Gmod 2013 Meeting Location Survey
  Hello, As we are trying to plan for next years GMOD meeting, we would like to decide between two...
• How To Combine Two Reference Genome (Files) In Galaxy?
  Hi all, I have two reference (genome) files. Let's say EAB_FB_MG.fa(total37972 sequences/contigs...
• Interpreting Stats output of SAM tools
  Would greatly appreciate if someone can explain to me the difference between the two BAM summary ...
• How to determine genome wide Co-occupancy between two transcription factors? by Galaxy main
  Hello: I am currently using Galaxy to analyze several sets of ChIP-Seq datas, including those pu...
• ChiP Seq Track height and scaling in UCSC Browser
  Hi all, I recently work on several ChIP-seq data sets. My traditional workflow is .fastq/.fastq....
• How can one adjust sensitivity and the extent of mismatch between reference genome and target sequences in a data set when using HISAT2 aligner?
  I have two questions concerning the HISAT2 tool installed in Galaxy: 1. How can I increase sens...
• Converting a CuffData.db file into a .tabular or .csv or .xls
  Hi everybody, I need some help here. I made a scatterplot using cummeRbund from a cuffData.db fil...
• MUMmer dot plot error
  Dear all, I have installed into my local Galaxy the tool Mummer dot plot, I have an error that  ...
• Mean Inner Distance
  Hi Vanessa, Mean inner distance can be thought of as being the estimated gap left between the tw...
• Rv: Visual And Conputational Analysis Of Positive Sites In Chip-Chip Data
  Hi all We are working with chip-chip data of S. cerevisiae (from Affymetrix) and actually we hav...
• sum all but first 500 lines
  I'd like to make a genome coverage distribution plot using the X-Y plotting tool X = coverage de...
• How to export the SNPs between whole genome alignments using the command line?
  I am using Mauve to align two the whole genome sequences, one of the sequence is in the form of c...
• multibamsummary vs multibigwigsummary
  I am in the process of comparing the similarity between two ChIP-seq conditions. According to the...
• Wrong axis labelling of CummeRbund scatter plot
  Hi all, I am plotting my CuffDiff results in a scatter plot using CummeRbund. Without log10 tran...
• Finding Snp Differences Between Datasets
  Hi, I am trying to find SNPs and/or indel variants that differ between two groups of samples. Th...
• How to choose values in trimmomatic steps ?
  which one file to choose the adapter sequences to use and what are the value to choose for Maxim...
• Deconvoluting Ngs Samples With Multiple Barcodes
  Hi, I have a sequence file that has 454 reads for 64 barcoded samples. I also have a second 'qu...