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• Upload fails for larger file, followed by FASTQ to FASTA conversion error
  I am trying to generate a FASTA file from a FASTQ file that was generated on an Illumina MiSeq. ...
• TopHat align summary
  Hello, I am using galaxy to analyze RNA seq of 100bp sing end data, sequenced with Illumina 2500...
• Using Segments Of Sequences As A Reference Genome - Bowtie For Illumina
  Dear all, My problem seems like something that should have a very simple solution from my end and...
• Transfer FASTQ data from external resource to Galaxy
  Dear all Please how can I transfer a FASTQ file directly from Illumina basespace to Galaxy? Thank...
• Server Error - Help Please
  Hi, I am trying to use Galaxy to (1) obtain a multiple alignment file from the genome browser, a...
• Need help with "Map with BWA for Illumina" tool
  Why can't I import my fastq file from my history? I am in the history with all files - gDNA reads...
• Expected Transcriptome Blast
  Hey, Jack Colicchio here, a PhD. student at KU. I am about to get an illumina Next gen transcri...
• cannot align my fastq files
  i have two data sets of fastq type but i cannot align them with any aligner on galaxy tools as no...
• Correct way of merging samples for father, mother, child trio variant calling
  I am new to NGS data analysis and I'm working in a multiple-sample variant calling workflow. I ha...
• Uploading multiple FastQ files from BaseSpace to Galaxy
  Hi, Hoping someone can help. I have a run that recently completed on our Illumina MiSeq and the ...
• Using BWA with Illumina data and metagenomic "reference genome"
  Hi, I'd like to try using BWA to align Illumina reads to some contigs a collaborator made from my...
• Server Error - Help Please
  Hi, I am trying to use Galaxy to (1) obtain a multiple alignment file from the genome browser, ...
• Problem running Clustal 2.1 Multiple Sequences Alignment - an instance of 'std::bad_alloc'
  Dear All, I've been trying to analyze reads from a short transcript. The data I have was obtaine...
• Internal Fail error 500 or file failed
  What am I doing wrong? My files have an extension of .fastq. I am told that these files contain r...
• Uploading Illumina Bam Files In Galaxy
  Dear Galaxy Users, I had a quick question as a new Galaxy user. I just received WGS data from I...
• Alignment and consensus from mapped reads (Ion PGM - Ampliseq Custom Panel)
  I have an Ion Torrent Ampliseq Custom panel of 28 Culex genes that I have run on our Ion PGM. It'...
• Which Galaxy tool can concatenate fastq files from different lanes of flow-cell?
  Which tool on Galaxy can I use to merge my fastq files from lanes 1,2,3, and 4 of a single librar...
• Galaxy -- use of MinION data to convert FastQ to FastA
  Hello, I have FastQ data from the MinION and I am having troubles converting these FastQ files to...
• not select Fastq File
  I get data (Fastq File Illumina), but when I would like to use Fastq summary statistics (NGS>Q...
• 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...
• Unable to convert FASTAQ file into NCBI standered FASTA file format
  Hi I wanted align multiple alignment of several Salmonella Typhi isolates in bioedit software. I ...
• Fw: Change Format With "Edit Attributes"
  Hi Peter, Thank you for your fast answer. I just want to know how can I use output files from B...
• Analyzing ChIP-seq data from HiSeq 3000
  I have acquired ChIP-seq data from an Illumina HiSeq 3000. I have followed the analysis workflow ...
• Workflow to clean data prior to variant call
  Hi,  I would like some advice on the workflow I'm using. 1- I have WGS data from bacteria, I've...