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• Extract/analyze base quality scores of mutations from BAM alignment
  Hello, I have RNAseq data aligned to my reference genome in BAM format. I would like to correlat...
• parameters and library type for tophat
  hi i haev SRA ids on which i am working. i plan to generate a reference based assembly. 1. i ha...
• multiBamSummary in DeepTools_sample order did not match to the entry
  Hi Everyone, I tried to plot the correlation plots using the DeepTools on the web base Galaxy. ...
• A Question Regarding Sequence Retrieval
  Dear Galaxy, I have the results for the sequence retrieval for Insulator ...
• ChIP-Sequencing data analysis
  Hello, I am trying to analyze ChIP-Seq data and extract enriched motifs from it. I have done the...
• Is there an alternative tool to plot RNA-Seq differential expression than cummeRbund?
  I have some results from cuffdiff to plot but I cant use the cummeRbund, is there another tool ...
• MNase ChIP-seq paired-end data analysis ?
  Hello everyone! Sorry for long explanation! I did paired-end ChIP-seq for my input and IP sample...
• Processing Multiple FastQ files to obtain an expression matrix
  Hello,    As a learning experience I am playing around with RNA Seq fastQ data. My goal is to s...
• What to do when alignment rate is low even though the genomic data and RNA-seq data are of same stain
  Hello While doing RNA-seq analysis, when I mapped reads for each condition to the reference gen...
• How to know if mapping to reference genome was succesful?
  Given a set of BAM files for single-end reads just mapped with BWA tool, how can I have an overvi...
• Questions Regarding Circster Visualization
  Hi, I just noticed that Circos plots are now incorporated into Galaxy's visualization methods wh...
• Analysing paired end RNAseq data with poor quality score
  Hello, I'm new in NGS and i'm currently working on RNA-seq. I had 6G of illumina reads and proce...
• RNAseq data to be processed in two ways: (i) mapping to de novo Trinity-based transcriptome and (ii) mapping a relatively new genome
  Hello all, I am new to RNAseq data and learning this process step by step, so I have a few quest...
• mapping RNA-seq reads with "N" in the middle of each read
  Hi all, I am performing differential gene expression analysis using the Tophat-Cuffdiff protocol...