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• gtf files for xenopus in galaxy instance
  Galaxy has Xenopus tropicalis genome XenTro9 vesrion for alignment, which annotation file (gff or...
• Alignment Coordinates
  Hello, I imported a sequence alignment file from clustalw. How can I generate a list of the coor...
• Bacterial RNAseq in Galaxy
  Is there a workflow to follow alignment of bacterial RNAseq. I want to align FAStq file and then ...
• 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...
• 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...
• error using HTseq-count for conversion of .bam to raw counts
  Hello, I am trying to convert the .bam files I got as output from tophat alignment into raw coun...
• Trimmomatic output results in extremely low alignment using bowtie2
  Hello, I have trimmed by paired end data RNA seq (Illumina Miseq) data using trimmomatic. Howeve...
• Tophat Alignment Statistics?
  Hi, galaxy users How to get Tophat alignment statistics such as % of reads aligned to exon, intr...
• Where to find Bowtie2 output stderr filehandle?
  Dear all, I want to find the alignment rate as suggested in bowtie2 "standard error" ("stderr") ...
• Number of sequence reads
  Is there a simple way to determine the number of sequence reads in a file uploaded on Galaxy and ...
• bowtie aligner does not see my fastq file?
  Although I could see that the RNA seq data has been uploaded as fast file in the history, I could...
• GTF file is not recognized
  Hello, I am trying to align my hits with a GTF file that I upload from Ensembl, however it is no...
• What to do when alignment rate is low even though the genomic data and RNA-seq data are of same stain
  Hello While doing RNA-seq analysis, when I mapped reads for each condition to the reference gen...
• 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...
• How to align sequences with MAFFT
  I want to align two FASTA sequences. I am trying to use MAFFT , Multialign tool in Galaxy. Doe...
• 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...
• BOWTIE BAM file alignments
  I prepared a small RNA (28-34nt) library made up of ribosome protected RNA fragments.  I prepared...
• Hitsat2: Spliced alignment options
  Hi, I am trying to analyze RNAseq data with HISAT2. I would like to include spliced alignment. I...
• 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...
• 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 ...
• 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...