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• Genome build accession for Galaxy build-in genomes
  How can I find exact genome build (NCBI accession number, like GCA_000001405.17) for build-in gen...
• Suppress Reporting Hit Number
  Hi, I used the Megablast function (in the NGS: Mapping\ROCHE-454\) to analyze my FASTA sequences...
• bowtie2 output only mapped reads --no-unal option
  Hi, I've been trying to run the galaxy bowtie2 tool and couldn't find an option to report only a...
• Commandline Bowtie2 and variant call help.
  Hello there! When you run bowtie2 to align the reads to the genome, some stats about the file ar...
• Bacterial Sequence for Variant Analysis
  I am analyzing paired-end data for bacterial genome and have done the following steps: *FAST...
• Bowtie-build : Finding information from bowtie2 indexed genome file
  Hi all! I did a bowtie2 index on a genome file using bowtie2-build. How do I find the following ...
• How to get only paired end or single end uniquely mapped reads with Bowtie2?
  Hello, I am using bowtie2 on galaxy to map ChIP-seq single end and paired end libraries to a ref...
• Trying to upload own reference genome to use in Bowtie2 and BWA aligner, having trouble with FTP filezilla
  Hello there, i am new to galaxy, and so far im loving all of the features. As a final year stude...
• Having problems using visualization-trackster
  Hello, I am attempting to align my Illumina MiSeq paired end (2x250) reads to 2 different refere...
• Help with bowtie2: reference genome for mapping is not listed
  Hi! my name is Leticia Perez and I am from Uruguay, School of Sciences, University of the Replub...
• Need to Expand Visualization
  Hello,  I recently used tophat2 to align two reads to the rn4 genome. I went through trackster...
• Yeast genome reference in Bowtie2
  I am trying to do some data analysis of my Chip Seq data in yeast. And I stuck at the alignment s...
• Tophat Settings
  Dear All, I am not so sure about two Tophat settings. Please help. 1) "Number of mismatches a...
• Are all the starting BED coordinates generated by BWA matching the first base of the reads ?
  I am currently using "Map with BWA for illumina" (in galaxy main server) with default settings to...
• Megablast
  I have a large set of short reads (from human) that I'm trying to analyze with galaxy. Specifical...
• RNA-seq analysis for a small number of genes
  Hi all, I am new to RNA seq analysis and want to look at the expression of a small number of gen...
• Rna Seq Analysis
  Hi I have a couple of questions regarding RNA seq analysis. My questions are 1.I need to use a v...
• Visualizing BowTie2 BAM File?
  Good Morning: I am new to Galaxy, and have a question about the BowTie 2 BAM file.  I had BowTie2...
• Use whole genome or cDNA sequences for RNAseq alignment
  Hello,    I'm working on my first RNAseq analysis, and I'm unsure of how to proceed with my TopH...
• Where to find Bowtie2 output stderr filehandle?
  Dear all, I want to find the alignment rate as suggested in bowtie2 "standard error" ("stderr") ...
• Upload Jatropha Reference genome for Bowtie2
  Hi Team Galaxy, I would kindly request you to upload Jatropha curcas reference genome in Galaxy ...