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• Question About Sicer Out Put
  I used SICR to call peaks and have following out put files: 1. test.1removed bed 2. control1 r...
• illumina PE quality control - NGS: QC & Manipulation
  Hi, I have a PE illumina miseq data set (separate forward-R1 & reverse-R2) of a WGS of a par...
• BAM file manipulations
  Hi I have made a whole assembly of RNA seq data using Trinity. The assembled file generated has ...
• "Deleted dataset" - from a dataset that isn't deleted.
  I am very very new to Galaxy and bioinformatics and have been trying to navigate my way through t...
• Help with interpreting RNA-seq output
  I am new to galaxy and have been trying to figure out how to align RNA-seq reads to a genome in o...
• Batch workflow with two different inputs each time?
  Dear Galaxy Community, I have actually installed Galaxy on our cluster, and I am now trying to d...
• data missing from visualized tracks
  Hello, I was browsing through my contigs, and I was looking for incongruities between different ...
• Issues with Using CuffDiff Tool in Galaxy
  Hi,   I am analyzing microRNASeq data. My pipeline is qc reads, bowtie for alignment, cufflinks...
• Chip-Seq Normalization To Total Number Of Reads
  Dear Galaxy, I am trying to analyze my ChIP-Seq data from Illumina using Galaxy. I have 2 datase...
• I want to know how data is normalized between control group and test group in differential rna seq analysis. Can somebody please explain or suggest some references
  I am a beginer in rnaseq data analysis. I want to know how data is normalized between control gro...
• Paired-end Reads trimming
  Hey there. I am starting to analyse some RNAseq paired-end data. At the pre-processing step I go...
• Can I Convert Paired-End Datasets Into Single End Ones?
  Dear All, I have some paired-end datasets to be analyzed, but I am not sure about their Mean Inn...
• DEseq2 replicate not normalizing
  Hi there, This issue has been posted about before but I couldn't find a definitive answer. I not...
• Problems with MACS peak calling--FDRs of 100%
  Hello, I am having some issues with MACS peak calling. I have 5 files in my ChIP-Seq dataset (in...
• What Is The Minimum Quality Should I Set For Filter Fastq?
  Dear All, I am analysing RNA-seq datasets for differential splicing events between cell types. ...
• Do I need to normalize the ChIP-seq BAM files before run MACS?
  Hi Everyone, The experimental ChIP-seq datasets I am analysing have two times of aligned reads t...
• This job was terminated because it used more memory than it was allocated (new post)
  To Galaxy, I've read on this forum about the proposed solutions to this memory issue. Other than...
• Can I Plug In Java Code Tools In Galaxy?
  Hi, (Am new to Galaxy) I am analyzing the Galaxy tool to find out the feasibility of plugging in...
• Data From History Now Showing Up In Fastq Drop Down
  Hi All, We have a galaxy local install. Thanks to Carlos's suggestion, I was able to get the ref...
• HTML display problem on Galaxy v17.09 with Bismark Pretty Report
  Dear Galaxy Community Since my recent upgrade to Galaxy v17.09 (from version 17.05), I am having...
• Extract fastq sequences from BAM with flag Supplementary alignment
  Dear all, after running BWA-MEM on a fastq dataset, I identified some "supplementary alignment" r...
• TOPHAT error: segment-based junction search failed with err =-6 what(): std::bad_alloc
  Anyone know what this error is about or how to troubleshoot? Most samples work fine, but some thr...