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  Hi, I'm using the Varscan tool to call SNPs and INDELs. There are some TRUE variants that are no...
• Peak Calling on BED files
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• Calling a tool from bioblend
  Hi, I am trying to call a tool from bioblend: tool_inputs = {'input': vcf_ds['dataset_id'...
• Path Issue In Xml Tool File
  Hi, while defining my own XML tool (.../galaxy/tools/my_tool.xml) I need, apparently?, to have ...
• mpileup calling every ALT <X>
  Im using the mpileup application on galaxy and every base is being called with the ALT . It has 1...
• Custom tool produce empty outputs
  Hello everyone. I'm new to both Galaxy and python, so forgive me if my issue turns out to be si...
• p-value threshold varscan
  I'm trying to identify polymorphisms in three samples. I'm usng Varscan and the default p-value t...
• Macs- Duplicate Reads Removal
  Hi, Does MACS remove duplicate reads automatically during the peak calling? I'm running controls...
• Mpileup with vcf output?
  Hello, I noticed that the "mpileup" tool that gives an output file in vcf format is no longer av...
• Excluding promoter and exon peaks
  Hi, would appreciate if someone could advise me on how to exclude promoter and exon peaks after p...
• alignseq_seq.loc file missing
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• where to write Controller class in Galaxy Visualisation plugin
  Hi, I am developing a Galaxy Visualisation plugin(new to galaxy). I have written a basic mako fi...
• Galaxy Cloudman - Nodes Can'T Make Their Own Qsub Calls?
  Hi guys, I created a new Galaxy instance web launcher (https://biocloudcentral.herokuapp.com/lau...
• Tool failure that reports: AttributeError: 'module' object has no attribute 'ICM'
  Hi, I want to run Tuxedo2 workflow associating cufflinks with a gtf annotation file. TopHat se...
• MACS2 input not recognized by tool
  Hi all, I've been using Galaxy to analyze my ChIP-seq data, and have managed to get the program ...
• 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...
• Problem with Refreence Genome in Gatk Tools
  Hi, I am attempting to run a variant call on Gatk. I used the "Validate Variants" tab first, how...
• Sicer Dose Not Support Chicken Genome
  Hi all I just found that I could not use sicer to call peaks from chicken data. It says 'sicer do...
• built pvulgaris genome
  Hi I'm struggling with the SNP discovery. I've tried to add the reference genome to run naive va...