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• Cuffdiff-output-couldnot find fasta record for a scaffold
  Dear Galaxy team When i ran cuffdiff for my merged transcripts file using a custom reference gen...
• How to assemble scaffolds using Galaxy
  I haved downloaded scaffold sequences from the Internet. Can I use Galaxy to assemble the scaffo...
• Is there a problem with the QUAST tool?
  I've attempted to use QUAST several times since yesterday (I tried once more this morning), but i...
• Cuffdiff Without Gene Annotation
  Hello guys, I went through the RNAseq workflow (I didn't do Cuffmerge) and from the Cuffdiff outp...
• Create Circos Builder
  Dear all, Does anyone used Circos builder via usegalaxy.?. I do not know how to get the **Cytoge...
• Workflow variable rename not working
  Hi, I use constantly dataset renaming in my workflows but I have a case where there might be a b...
• Test.G2.Bx.Psu.Edu
  Hi, if you check the history stored as "7.26" under the account yuz111@psu.edu, you will find I e...
• Bowtie for Illumina using reference genome of pisifera oil palm tree
  How I can map reads against pisifera oil palm tree genome or against scaffolds? Thank you for a ...
• Scaffold from Blast results
   Hi All I have been struggling to get my head around how to create Scaffolds. I have created a d...
• How to download blastn to scaffold from toolshed?
  Hi I am using galaxy for my RNA seq analysis. I have made a metatransciptome and used this for d...
• annotations with genome of reference
  hi, Dears I am working with RNA-seq and i dont understand how create a de novo transcriptome usi...
• Problem with custom reference genome
  Dear all, on our local galaxy-docker-stable instance I would like to include additional referenc...
• data manager problem - building Bowtie Index for hg19
  I am testing out the process of setting up a local galaxy host - for analysis of clinical exome s...
• Glitch In .Wig Visualization In Trackster?
  Hi everyone. I'm having an issue with a wiggle file. I'm using Trackster on the public-main ins...
• Extract Genomic DNA using coordinates from a gff file
  Hi, I have been extracting genomic sequences, using "Extract genomic DNA" from "Fetch Alignment...
• SAM to BAM of samtools: It can't find built-in reference genome.
  as the title! I installed data manager of samtools index builder. What a strange affair! SAM_to_B...
• Stitch maf Blocks Returns All Gaps
  I am trying to use stitch gene blocks on a pairwise alignments I generated using progressivecactu...
• Data manager for Bowtie for illumina (bowtie1)?
  Is there a bowtie1 index builder? I cant find it in data managers? If not how I can add indexes f...
• TopHat with Culex quinquefasciatus genome
  I try to use TopHat for RNA-seq data. The Culex quinquefasciatus genome will be used for the TopH...