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• Fastq File Generated By Samtools Can'T Be Recognized
  Good day. I'm trying to use Galaxy's FASTQ to FASTA converter. However, the fastq file I generat...
• Custom tool creates output in a directory -- how to make the user interface aware of it?
  Hi all, I have a perl script I am trying to integrate into a galaxy server. The script generates...
• 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...
• making galaxyIndices volume smaller in cloud by deleting genomes
  I wish to remove most of the mnt/galaxyIndices/genomes files so I can have a smaller volume that ...
• Fasta Generation From Pileup For Snp Detection
  I'm interested in generating a fasta file from Ilumina paired reads of my wild type strain. I hav...
• Can't obtain overlapping Peaks
  Hello, I've generated peaks using MACS2 for H3K4me3 and H3K27me3 and now want to find the overl...
• in silico AsiSI digestion of human genome
  Hi, I need to generate a file with the coordinates of sites in the human genome from an in silico...
• Filter BAM app in Bam Tools
  I'm trying to eliminate inserts larger than 500 bp in a Bam file generated by Bowtie2 using the F...
• Question About The Gatk Tools
  Hi, I just uploaded the BAM file for an exome sequencing sample and was trying to use the GATK t...
• Pileup error: line length exceeds XXX in sequence YYY
  Hi,    I mapped my reads, filtered unpaired reads, converted to BAM and now I want to generate ...
• Maq Output
  Does anyone know if Maq can produce alignment data in SAM format? Currently we can only generate ...
• Adding a reference genome to a local Galaxy
  Hoping to find some Galaxy Dev team experts. I am trying to add hg38 to the HiSat2 tool so that t...
• Downloading job's results fail
  I recently ran a job on the Galaxy server using the 'Extract MAF blocks'.  The run was performed...
• Jobs on local galaxy instance stuck in "New" state - Data Library datasets to blame?
  After updating our Galaxy instance to use two processes (one for web, the other as a job handler)...
• Barcode splitter error "Can't locate Data/Dumper.pm" - ticketed issue, see answer for details
  Hello everyone! Here's some promlem with barcode splitter in usegalaxy. I want to sort my fastq ...
• Can I generate random output file in galaxy using XML command Tag
  Hii  I integrate the SoftSearch tool in galaxy project it will generate .vcf file but i want to ...
• "Viewing" excel files in local Galaxy
  Hi, On my own local instance of galaxy when I have an 'xlsx' file and click the eyeball to view ...
• TOPHAT align half of the reads
  Since I am using a laptop, I'd like to exploit usegalaxy to perform an alignment using tophat. I ...
• upload file through ftp
  Hi, I have been trying to upload a file (29.5G) through ftp. When click "choose FTP file", I can...
• Upload data by FTP in Galaxy
  Hi everyone, I'm trying upload some data in Galaxy by FTP but I have the files in my FTP account...
• Using DiffBind in Galaxy to generate PCAs of ChIP data
  Hi all, I'm trying to use DiffBind in Galaxy to make a PCA or multiple ChIP-seq sets. I have the ...
• DiffBind: Generating a PCA in Galaxy
  Hi all, I'm trying to use DiffBind in Galaxy to make a PCA or multiple ChIP-seq sets. I have the ...
• Why Is 'Filter Pileup' Not Recegnising My 'Generate Pileup' File?
  Hi, I was wondering if you could help me with a problem I have been having recently. I have ca...