Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • Demultiplexing qseq

    Hello everyone I received data from Illumina sequencing into qseq files from different LANE.

    And barcode for different samples.

    SO I tried to transform my qseq files into fastq and then use fastx_barcode_splitter.pl to demultiplex by the barcode tag, but I am retrieving less reads.
    I want to know if there is another strategy to demultiplex.


    Best Regards,
    Last edited by shadow19c; 04-10-2014, 11:58 PM.

  • #2
    How many fastq files with reads do you have per lane? Did you use barcoded Truseq adapters or what type of adapters? Did you provide the barcode data in the correct orientation (perhaps the reverse complement should be used in your case?

    Comment


    • #3
      Hello,
      So i have 20 .qseq files for each lane (3 Lanes).
      So I transformed my 20 qseq files into one fatsq file, finnaly I have 3 fastq.

      What do you mean
      the reverse complement should be used in your case
      Best Regards,

      Comment


      • #4
        I have a tiny perl script here doing this job, qseq to fastq. PM me if you are interested.

        best,
        Sven

        Comment


        • #5
          Hi luc,
          In which ocasions should one use the reverse complement?
          I am looking at demultiplexing some data, and there are NO reads matching my barcodes. When I run FASTQC it seams like there are multiple sequences that would match the reverse complement of the barcode.
          please have a look at my post: http://seqanswers.com/forums/showthread.php?t=45234

          thanks

          Comment


          • #6
            Hi Ines,

            Have a look at the following webpage from U. Texas at Austin, it may help.


            Comment

            Latest Articles

            Collapse

            • seqadmin
              Essential Discoveries and Tools in Epitranscriptomics
              by seqadmin




              The field of epigenetics has traditionally concentrated more on DNA and how changes like methylation and phosphorylation of histones impact gene expression and regulation. However, our increased understanding of RNA modifications and their importance in cellular processes has led to a rise in epitranscriptomics research. “Epitranscriptomics brings together the concepts of epigenetics and gene expression,” explained Adrien Leger, PhD, Principal Research Scientist...
              04-22-2024, 07:01 AM
            • seqadmin
              Current Approaches to Protein Sequencing
              by seqadmin


              Proteins are often described as the workhorses of the cell, and identifying their sequences is key to understanding their role in biological processes and disease. Currently, the most common technique used to determine protein sequences is mass spectrometry. While still a valuable tool, mass spectrometry faces several limitations and requires a highly experienced scientist familiar with the equipment to operate it. Additionally, other proteomic methods, like affinity assays, are constrained...
              04-04-2024, 04:25 PM

            ad_right_rmr

            Collapse

            News

            Collapse

            Topics Statistics Last Post
            Started by seqadmin, 04-11-2024, 12:08 PM
            0 responses
            59 views
            0 likes
            Last Post seqadmin  
            Started by seqadmin, 04-10-2024, 10:19 PM
            0 responses
            57 views
            0 likes
            Last Post seqadmin  
            Started by seqadmin, 04-10-2024, 09:21 AM
            0 responses
            51 views
            0 likes
            Last Post seqadmin  
            Started by seqadmin, 04-04-2024, 09:00 AM
            0 responses
            56 views
            0 likes
            Last Post seqadmin  
            Working...
            X