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• Maf Alignments
  Hi Galaxy, Can you please enlighten me on the concept of MAF alignments ? Are th...
• Galaxy for alignment for genomes of bacterial species
  Galaxy can be used for alignment for genomes of bacterial species or not?? How genome sequence ca...
• Alignment rate differes using hg19 and hg38
  I have some RNA-seq fastq files.I'm using HiSat to align the fastq files. To do so, I use the bui...
• Tophat Alignment Statistics?
  Hi, galaxy users How to get Tophat alignment statistics such as % of reads aligned to exon, intr...
• gtf files for xenopus in galaxy instance
  Galaxy has Xenopus tropicalis genome XenTro9 vesrion for alignment, which annotation file (gff or...
• cannot align my fastq files
  i have two data sets of fastq type but i cannot align them with any aligner on galaxy tools as no...
• Bacterial RNAseq in Galaxy
  Is there a workflow to follow alignment of bacterial RNAseq. I want to align FAStq file and then ...
• miRNA sequencing alignment
  i have a rna-seq data and would like to align it against micro RNA human. Can I do it in galaxy. ...
• SHRiMP2 aligner as part of NGS: Mapping
  Is there anyway SHRiMP2 can be put on the public galaxy server as a part of the NGS: Mapping tools?
• tophat multi read alignment
  Hi, How to do --prefilter multi read hits in Galaxy TopHat Regards Lakshman
• Galaxy Bowtie Alignment Stats Report
  Hello, Does anyone know how to get alignment stats from Bowtie on Galaxy? I would like to know w...
• where is locally cached sequence/ alignment data in Galaxy?
  Hi, Does anyone know how to access the locally cached alignment files (MAF)? On the website: Unde...
• Number of sequence reads
  Is there a simple way to determine the number of sequence reads in a file uploaded on Galaxy and ...
• Aligning a file with many protein sequences to a reference genome in galaxy
  I am trying to align a FASTA file with 2200 protein sequences to a reference protein sequence in ...
• How to align 500 fastq unpaired files to an uploaded reference and put every single result to a new folder?
  How to align separately 500 fastq unpaired files to an uploaded reference and put every single re...
• Alignment going very slowly
  Hello. Are there issues with Galaxy today" I have been running some alignments for 2 days now, ...
• 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...
• 100-way multiZ alignments (with hg38 as reference)
  Hi I am currently using GRCh/hg38 as my reference. I would like to inquire if there is 100-way m...
• Chromosome alignment to generate MAF file
  Hello, Can I do a chromosome alignment or do I need to use other softward like LASTZ, LAST or MU...