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• Error from HISAT2 when using fasta data retrieved from Get Data: EBI SRA
  I have uploaded files from EBI then I run the HIST with the following setting Source for the re...
• Joining overlapping paired end reads
  Dear All,   I have DNA sequencing data (targeted sequencing) produced by MiSeq. The size of the...
• Galaxy Cloud: Location Of Imported And Converted Fastq'S
  Hi, I had fastq.gz files in an Amazon S3 bucket. I created a Galaxy on the Cloud instance usin...
• Mapping paired reads to reference genome, variant calling
  I am trying to map a trio of paired-end Illumina reads to a reference genome, then identify polym...
• Trinity run preprocessing
  I am new to Trinity and galaxy instance (https://usegalaxy.org/). I have 17 samples pair ended. I...
• Preprocessing Gdna Illumina Paired End Data For Mapping/Snp Calling
  This question is w/ regards to pre-processing whole genome resequencing data for mapping data to ...
• fastq.gz file can not auto uncompress
  I uploaded two fastq.gz files to usegalaxy.org using FTP. The first one worked well. The second o...
• Decompressing files on local galaxy
  HI, I am using local instance of Galaxy. I have uploaded my dataset and they are in fastq.gz fo...
• FTP file upload not working
  I am not able to upload files using FTP onto the galaxy server. Many people have been facing this...
• Fastq.gz files taking a long time to upload
  Hello, I am trying to upload two files, both of which are about 2.4 GB and in fastq.gz format. I...
• Pair end alignment using HISAT2
  Hi, I have a FASTQ file that is a paired library. I want to align this FASTq file to Hg19 genome...
• Memory allocation error while trying to align paired end reads using RNA STAR
  Hi This is my first time using Galaxy for RNA Seq analysis. After uploading and normalizing my r...
• Bowtie 2 output read
  I am using galaxy platform to run Bowtie 2. I have illumina paired end reads (file#1 and file#2)...
• Making paired-end reads the same length
  I have paired-end data (in two separate files).  I have groomed my files, and would like to filte...
• Kraken (assign taxonomic label...)
  One Illumina file fastq.gz contain all info about paired-end reads. I used by usegalaxy interface...
• Splitting Biased Paired End FASTQ data
  The FASTQ splitter in Galaxy warns that the tool only works if Paired-end data has equal length r...
• Pre-Processing Of Illumina Rna-Seq Paired End Data
  Hello, I have Illumina 76bp paired end data for a zebrafish RNA-seq experiment and am basically ...
• FASTQ Joiner or Interlacer problem
  Hello everyone, I am trying to use the FASTQ interlacer or joiner on my pair end read files. Aft...
• Merging Of Illumina Paired End Files
  I have 3 illumina paired end reads of exome capture of the sample. I want to assemble these reads...
• Is my fastq file broken
  Hi Biostar My question is when I uploaded my fastq file to galaxy, it can not go to groom. Norma...
• FTP upload is crashing with large files (3GB)
  Anyone had trouble uploading large files to galaxy FTP? It is my first time, I am trying to uploa...
• 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...
• Which file must be used for assembly?
  I want to assemble a genome using de novo assembly and I am very new to it. The Illumina sequenci...