Similar posts • Search »

• 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...
• Galaxy showing and hiding tools as refreshed?
      I have installed some tools, but when I click on Galaxy logo and on Analyse data I see tool...
• Rna-Dna Converter In Fasta Format
  Hi all, I want to to map my sequencing reads to miRNA reference database . Anyone know how to con...
• Question
  Hi Is it possible to trim a variable number of a specific nucleotide from the 3' ends of fastq R...
• Filter for sequencing reads mapped to multiple loci
  Hello I have done both a hisat2 and tophat alignment, both yielding BAM files which I later con...
• Displaying Bed Files In Ucsc
  Hello, I have a bed file in this format: chr# start end scores. I tried to view it in ucsc main...
• How can I do trimming off to all nucleotide sequences that end with a specific sequence in my illumine reads?!
  Hello everyone, I am new to Galaxy and I was wondering if anybody knows how can I trim all seque...
• convert annovar in excel to vcf for igv viewing
  Hello, In an excel file I have the chromosome, start and stop positions, reference allele (Ref),...
• Viral mapping of new strains within host samples
  We have conducted NGS run on Ion Torrent looking for presence of unknown viruses within host samp...
• How do I get reference genome?
  There is no reference genome for leishmania in Bowtie2 tool - map reads against reference genome....
• BAM to VCF format
  I'm analyzing NGS data on website:usegalaxy.org in the following steps: 1. Fastq file Raw reads Q...
• Mapping (with HISAT2 / Bowtie) on custom genomes yields always 0 matches
  Hi, I've the following problem. I'm using HISAT2 and Bowtie. I'm using a gene with 1200 nucleoti...
• Bowtie: Outputting Unmapped Reads
  I was hoping this question had been asked, but I haven't been able to find it. I want to output ...
• How Much Can I Trimm My Reads
  Dear All, I am analysing RNA-seq datasets for the differential splicing events between cell type...
• Megablast
  I have a large set of short reads (from human) that I'm trying to analyze with galaxy. Specifical...
• GWAS: Fastq to BAM to VCF
  I'm analyzing NGS data on website:usegalaxy.org in the following steps: 1. Fastq file Raw reads Q...
• Get multimapped reads from STAR in Galaxy.
  Hi, Using RNA STAR in Galaxy to map my yeast read back to the genome: (single end reads), I'm g...
• Mapping Paired End Reads With Tophat
  Hi all, After mapping, I used IGV to have a look at the mapping. There are a lot of mapped read...
• Troubles with full settings on Lastz
  Hi, I am new to bioinformatics and I have troubles using Lastz. I use it to detect a 39nt seque...
• extract only unique mapped paired end reads
  Hello,  I aligned paired end reads with bwa 0.5.9. Next, I would like to extract only paired end...
• How to convert ion torrent Reads into Wiggle by galaxy?
  Hello: I just obtained a set of BAM file that is obtained by Ion Torrent(our collaborator helped...
• Bowtie Reference Genome
  Dear galaxy users, I am trying to map some multiplexing bisulfite PCR data (Illumina) to o...