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• Diamond insufficient arguments on Galaxy
  Hello, I have DNA query sequences in FASTA (trimmed reads from RNA seq) that I want to align wit...
• Align.seq metagenomic data
  I am new to galaxy and i am using metagenomic data after unqiue.seqs step i use the unique.reads...
• Work with protein sequence in snpeff?
  Hi, I am knew to bioinformatics and I would like to know if it is possible to run the snpeff on ...
• Extract reads from BAM file
  Hi I have a BAM file with all the reads aligned to the reference sequence that I used to map them...
• Blast sequence using bacterial genome of ncbi
  Hello, I have installed my galaxy on local server and successfully and added NCBI BLAST plus. I ...
• Alignment Question
  Hello, I was wondering if Galaxy can align Solexa reads to a reference sequence. If not, can I u...
• Aligning more than 2 sequences
  I have a pair-end data fast1.fq and fast2.fq in (fastq format). Now, I need to align the pair-end...
• 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 ...
• Aligning Against Multiple Reference Sequences
  Are there any tools in Galaxy to align short reads against multiple reference sequences? I have ...
• Hmm Tool In Galaxy??
  Hi, Are there any tools like HMMER (2.3.2 or 3.0) available on Galaxy to run a HMM on a DNA or p...
• Problem running Clustal 2.1 Multiple Sequences Alignment - an instance of 'std::bad_alloc'
  Dear All, I've been trying to analyze reads from a short transcript. The data I have was obtaine...
• 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...
• BLASTing on the cloud
  I've not run a stand-alone version of Galaxy, nor a cloud-based one, at present.  However, I have...
• Stitching MAF blocks for use with phyloCSF
  If I've understood correctly - when using Galaxy's stitch MAF blocks tool, the resulting fasta fi...
• How to align sequences with MAFFT
  I want to align two FASTA sequences. I am trying to use MAFFT , Multialign tool in Galaxy. Doe...
• Using Tool On Input Data Set
  Hello, I'm new to Galaxy and have a very basic question.  If I upload a dataset, (say, a pr...
• Preparing for Blast2GO
  Here is my problem: I have used Cuffdiff to determine differential gene expression and extracted...
• use HIV as reference genome
  hi, i have 4  read outs that cover the whole genome of HIV sequence. i want to align them to for...
• Visualizing BowTie2 BAM File?
  Good Morning: I am new to Galaxy, and have a question about the BowTie 2 BAM file.  I had BowTie2...
• GFF Error: duplicate/invalid 'transcript'
  Hi There, I am new to the field of bioinformatics and faced some difficulty while using galaxy fo...
• Number of sequence reads
  Is there a simple way to determine the number of sequence reads in a file uploaded on Galaxy and ...
• Question about Alignment of barcode sequence
  For Ion torrent data (each read is like barcode sequence followed by target sequence) I tried to...