Similar posts • Search »

• Galaxy app to retrieve selected raw reads
  There are many previous threads regarding how to retrieve selected raw reads from fastq files off...
• Tophat Mapping
  Hi, After mapping RNA-Seq paired end reads with Tophat, I can see that most of reads fall into...
• sort reads by start position
  I did RNA sequencing and many reads map to tRNA regions. Specific tRNAs are completely covered b...
• Mapping using multiple reference sequences
  Hi I am using BWA to map my FASTQ files against two different reference sequences (V3-1 and V3-2...
• (No Subject)
  Hi Dear Is there anybody whom I can share my data with? I have an important question that I tried...
• (No Subject)
  Hi Dear Is there anybody whom I can share my data with? I have an important question that I trie...
• How can I improve my mapping alignment rate with MiSeq 2x300 bp paired-end reads?
  Edit 1: it appears I have misinterpreted the raw data, which in turn led to my poor results. The ...
• How many should multiple alignment of tophat-out in Human RNA-seqs?
  Hi I'm checking my tophat output data and I would like to know the rate of this multiple alignme...
• How To Use Collapsed Sequence Files In Mapping And Displaying
  I found that there is a "collapse" tool under FASTA manipulation, which will significantly shorte...
• Bowtie Reference Genome
  Dear galaxy users, I am trying to map some multiplexing bisulfite PCR data (Illumina) to o...
• Map With Bowtie
  Hi Colleagues, I mapped illumina sequences using Bowtie on Galaxy server, I could not locate the ...
• Creating consensus sequence after mapping
  Greetings, I would like to know how to create contigs, or DNA consensus sequence after mapping t...
• When displaying a BAM file in the UCSC browser, will all the data be shown?
  I have recently mapped RNA-seq reads to the sacCer2 genome using bowtie in galaxy. I then filtere...
• How do I convert numerals to nucleotides for RNA-Seq mapping?
  The FASTQ reads I imported from EBI SRA (SRR064843) appear to be numeric (0-3) rather than AGCT....
• isoforms with cufflinks
  i used the cufflinks tool to create the isoforms. how can i know how many isoforms were created? ...
• Table With Gene Count Reads
  Hi, I was wondering if there is any tool on Galaxy were I can obtain a table with how many rea...
• remove in mapping results the reads that aligned > 1 times
  I would like to remove from the BAM file after mapping using bowtie2 tool, the reads that aligned...
• How to upload a reference genome
  Hi!, I am a new user in the Galaxy project and I want to map my reads with a genome that is not i...
• How to judge the quantitativity of ChIPSeq?
  Hi, I have now been through my ChIP-Seq analyses with some success using the Galaxy platform up ...
• 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...
• Tophat
  Dear all, This might be a silly question, but I couldn't figure it out by myself :-((. Could you...
• 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...
• 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...