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• How do I get reference genome?
  There is no reference genome for leishmania in Bowtie2 tool - map reads against reference genome....
• using SamToFastq 1.136.0 in Galaxy workflows
  Hello, How can I connect in the workflow SamToFastq and Bowtie2 tools in Galaxy? I am trying to ...
• NGS:mapping against maize reference
  Hi, when I select NGS:Mapping / Bowtie2 or BWA, in order to align sequences from GBS against a r...
• Bowtie 2 output read
  I am using galaxy platform to run Bowtie 2. I have illumina paired end reads (file#1 and file#2)...
• 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 ...
• Listing genome reference
  Hi, I would like to map reads against genome reference but my genome of interest is not listed. I...
• How to add a genome indexed at https://usegalaxy.org to IGB (when it is not already natively included)
  Hello, I have been using Galaxy Main to map WGS data from E. coli. I have tried several mapping ...
• Creating consensus sequence after mapping
  Greetings, I would like to know how to create contigs, or DNA consensus sequence after mapping t...
• Can a genome that's been released be added so I can map against it
  Hi there, I will be mapping my RNAseq reads to a genome of interests soon. Mapping with Bowtie2 ...
• Aligning Against Multiple Reference Sequences
  Are there any tools in Galaxy to align short reads against multiple reference sequences? I have ...
• 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...
• Error with Bowtie2 mapping against rhesus monkey reference genome
  Hello! I am trying to align a fastq file (fastqsanger) with Bowtie2 against the built-in referenc...
• Reference genome absent
  Dear Biostar, For mapping our paired end reads against horse, we are unable to find a reference ...
• How to check unaligned reads?
  I have a pair end SRA files for which I have done FASTQc. The SRA files are then mapped against ...
• error long spanning reads Malformed
  Hi, I have ran the Tophat 2.08 version and I have obtained this "result".log [2014-09-10 09:47:...
• 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...
• Output files: "genome.*.bt2" file. What is it?
  Hi everyone, I ran Bowtie2, mapping my MiSeq reads against a plasmid (8kb) I had to find out if ...
• Reference Genome how does it validate
  I have a very basic question. We map the m-RNA sequence cDNA with the reference genome and then b...
• Bowtie2/Samtools files are not visualized with Trackster: Fatal error Exit code 255 ()
  I am trying to map 8 paired-end reads on to the same reference custom-build genome. Each of these...
• From Bowtie Mapping To Gene Names
  Hi, I have reads from Illumina paired-end run mapped against reference genome using Bowtie. Is t...
• I used tophat and give mistake Error: segment-based junction search failed with err =-5
  In my local galaxy , I used Tool Shed TopHat Gapped-read mapper for RNA-seq data (Galaxy Version ...