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• i cannot find the fastq files inside datasets of bwa-mem although present in history
  please help me in that i uploaded two fastq files into history and started bwa-mem to align them...
• Galaxy On The Cloud - Cannot Select Fastq Files When Trying To Run Workflow
  Hi Galaxy, I am a newbie to Amazon EC2 and have been carefully following the steps in the screen...
• Cannot select data sets in local galaxy sever
  Hey, So I've installed a local galaxy server in order to helpout processing some large data we h...
• Debup Bam ?
  I Just got back a set of aligned data sets that have been trimmed etc but the files I've received...
• Error with setting metadata
  Hi, I recently setup a TopHat alignment of my RNA-seq data, but when I use Cufflinks on this dat...
• Non-coding RNA feature type/attribute
  Hi! I am attempting to perform a htseq-count on a HISAT2 aligned read BAM file containing aligned...
• no fastq data set available
  Hi, New to this program. Have my files uploaded in the history and have also made a dataset. How...
• How to convert unaligned reads to Fastq format after initial alignment?
  I aligned my sample against human chromosome 19. Now I want to use the unaligned reads and align...
• Cannot select fastq data in Galaxy Trimmomatic
  Hi Galaxy-verse I am trying to open my uploaded paired-end MiSeq reads in Trimmomatic from withi...
• Multiple alignment for fastq files from illumina
  Can I make a multiple alignment in Galaxy with fastq data from illumina? Clustal tool only takes...
• Variant analysis using Galaxy - tutorials, example workflows
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• fastq data types
  Hi, I've done quite some searching and have found numerous posts on the fastq format versions. I...
• Problems in SNPs identification
  Hello   I am Viva I am using galaxy as a platform to identify SNPs in my datasets. I have two d...
• how to perform alignment using Hisat2
  Actually I have several questions to ask but I try to be very much to the point. I want to uploa...
• Errors in post alignment files
  Hello. I was trying to perform an alignment of data (Tophat) which had been run through Fast Gro...
• Should Fastq Files Be Merged?
  Hi, I have downloaded the fastq.tgz files for an ENCODE RNA-SEQ data and unpacked the files. The...
• HISAT2 gzip: input_r.fastq.gz: not in gzip format
  Hello, I have been trying to use HISAT2 to to align RNA-seq ENCODE data which I download on my de...
• Workflow Input data not recognizing the data set
  I have extracted workflow for ChIPseq analysis from my work history. When I call this workflow to...
• Low alignment for paired end reads using HISAT2
  Hello, I am new to processing and analysis of RNAseq data. I have recently completed a paired-en...
• 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...
• Low data conversion rate for BAM-to-SAM. Fix Database, Datatype, Sorting
  I have WXS fastq files from an illumina HiSeq 4000 paired end run- I uploaded them through FTP as...
• Poor overall alignment rates
  I am having problems with the alignment process for some data that I obtained through NCBI GEO da...