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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...
• Reference Annotation error using HISAT2
  I keep getting a reference annotation error when I run cuffdiff using HISAT2 alignment files. The...
• Use paired collection on wrapper
  Hi, I'm try to write a wrapper for a tool that performed subsampling of fastq file. The script i...
• Query for inputting Hisat2 BAM with dataset collections for Stringtie analysis
  Hi, I have data set collections ( 3 biological replicates) that I could run on HiSAT2 and I have...
• 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...
• Reapload a usable Readcount file?
  Hi All, I have a question, I try to compare two different runs of RNA sequencing. However the di...
• Bioblend error for conditional input
  Using the python bioblend package to send my job into Galaxy, I have an error when I try to send ...
• You are not allowed to access this dataset
  Hello everyone ! I have a strange behaviour on my histories and it is troublesome since it affe...
• Bioblend download bed/interval file : HistoryDatasetAssociation not accessible
  Hello everyone, I need to download a large amount of files from histories of different users. Th...
• Question About Fastq Groomer
  To Whom It May Concern: I am a new user to Galaxy. In the function of "FASTQ Groomer", I notic...
• Can't run files successfully using BWA-MEM
  Hi I am currently working on a course project. Using the main galaxy server, I am having issues ...
• Problems With Picard And Gatk Tools
  Dear all, I have been trying to analyze some recently acquired WGS reads (re-sequencing with MiS...
• Installing HISAT2 on Cloudman
  Hi Galaxy, I am trying to install HISAT2 from the toolshed to my Cloudman instance (revision da2c...
• Metadata Error When Using Megablast
  Hello, I am attempting to megablast a FASTA file containing ~45,000 records of 100nt each agains...
• BWA for SOLiD
  Hello: I am receiving an error trying to perform the "Manipulate FASTQ" on my .fastq file. My or...
• Encoding problem with return value from tool's custom dynamic_options function
  Dear Biostars community, I am having problems developing a python function to return some custom...
• HISAT2 program does not complete
  Hello, I'm having the same problem--my HISAT2 programs fail to complete after days of running. ...
• Linked inputs in created workflow
  I have created a workflow with 9 steps. When I run my workflow the first 2 steps are to input dat...
• An error occurred setting the metadata for this dataset
  Hi Galaxy Team, I've been using TopHat to map my reads and I've received the same error message ...
• Samtools error assoicated with multiple mapping tools
  Hoping for some help here. I am having issues with several mapping tools that utilize samtools a...
• Upload fails for larger file, followed by FASTQ to FASTA conversion error
  I am trying to generate a FASTA file from a FASTQ file that was generated on an Illumina MiSeq. ...
• Data import from EBI SRA to Galaxy does not work
  Dear Galaxy Team, There seems to be a persistent problem with importing fastq files from EBI SRA...