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• Reference genome from data visualization
  Hi What I have seen in the tutorials is that you can see the FreeBayes results in IGV but only a...
• Loading VCF into a local IGV fails with metadata error during data prep step
  Although my genome sequence is part of the list of options thanks to custom build, the link to di...
• Creating gVCF using Galaxy Tools
  I am trying to use Galaxy tools to create gVCF file to be used for building gd_SNP file format. T...
• How do I determine the correct filtering threshold in VCFfilter after running FreeBayes
  I would like to perform a VCFfilter on my FreeBayes data but I'm not sure how to choose the corre...
• SnpEff database build tool for C.elegans
  I am trying to use the SnpEff build database tool to build reference genome for C.elegans and use...
• Trackster Error
  Hello, I am trying to look at an output from Tophat using Trackster, but I keep getting the foll...
• Bam To Bigwig
  Hello, I am trying to convert a BAM file to Bigwig using the Convert Format option under Attribu...
• Liftover tool not working at UCSC
  Hello, I tried to convert hg18 coordinates in a BED format data with UCSC liftover and it is not...
• Question About Unified Genotyper
  I have been trying to use either Unified genotyper or Freebayes on one of the Bam file. Both are ...
• Tools appearing/disappearing from tool panel (FreeBayes and BamLeftAlign)
  Hi All, I am seeing a problem where the tools FreeBayes and BamLeftAlign (under the NGS: Variant...
• Cuffdiff Question About Using An Unspecified (?) Database/Build
  Hello! I have an RNA-Seq project which consists of 5 samples from the species tr...
• Creating A Trackster Visualisation From A Reference In Your History
  Hi, I’m struggling to figure out how to visualise a SAM file in Trackster as a normal user (i.e. ...
• Annovar is returning a file with only headers
  Hi I am trying to do some variant analysis. I have mapped the reads using hg19 as reference thr...
• wig to bigwig format in galaxy, unavailable genome
  Hi, I would like to convert a .wig file to a .bigwig file. Should be straightforward, but I am...
• Error executing tool: maximum recursion depth exceeded while calling a Python object
  Hi, I'm using a custom genome (in FASTA format) which I downloaded from EupathDB.org. I used User...
• Error while visualizing FreeBayes.
  Hi, I'm trying to visualize my FreeBayes results on IGV or UCSC, but while Galaxy tries to transf...
• Getting an excel list of variations from Varscan or FreeBayes .vcf files
  I have whole genome sequence from Saccharomyces cerevisiae strains and I'm looking for their vari...
• How to I add a genome to Database/Build?
  Hi! After pileup file generation and convertion of pileup to interval, potentially we could extra...
• Solution For: Error Running Cuffdiff. Error: Cannot Open Reference Gtf File Condition, Control For Reading
  Hi, I ran into this error running cuffdiff. I had a hard time debugging this user error, so I th...
• Can I run the megablast against my own database?
  Hi, I'm trying to fish out antibiotic resistant genes from a hiseq data generated from human sto...