Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • qseq to fastq - post conversion quality trimming

    Hiya!

    I have a bunch of old RNAseq data sets that I want to re-analyse using our current pipeline. First challenge was that the data is old enough to have been archived in qseq format, not fastq. I converted all files using a neat little java tool found here:

    Free, secure and fast downloads from the largest Open Source applications and software directory - SourceForge.net


    Described here: http://www.biostars.org/p/6682/

    Has worked well and is pretty fast. My resulting fastq files, however, contain every single read - including the one with low quality and those that have a failed p/f flag. Therefore I want to some quality trimming before I move on to analysis.

    Does anyone have any tool recommendations? And, more importantly, a rational way of filtering? What would be a good quality cutoff to use? If I am not mistaken the quality scores spit out by the java tool are phred64.
    Cheers!

    TabeaK

  • #2
    qseq to fastq - post conversion quality trimming

    Trimmomatic is good for trimming Illumina data in fastq
    format.

    http://www.usadellab.org/cms/index.php?page=trimmomatic.

    Best wishes,
    Maria

    Comment

    Latest Articles

    Collapse

    • seqadmin
      Latest Developments in Precision Medicine
      by seqadmin



      Technological advances have led to drastic improvements in the field of precision medicine, enabling more personalized approaches to treatment. This article explores four leading groups that are overcoming many of the challenges of genomic profiling and precision medicine through their innovative platforms and technologies.

      Somatic Genomics
      “We have such a tremendous amount of genetic diversity that exists within each of us, and not just between us as individuals,”...
      05-24-2024, 01:16 PM
    • seqadmin
      Recent Advances in Sequencing Analysis Tools
      by seqadmin


      The sequencing world is rapidly changing due to declining costs, enhanced accuracies, and the advent of newer, cutting-edge instruments. Equally important to these developments are improvements in sequencing analysis, a process that converts vast amounts of raw data into a comprehensible and meaningful form. This complex task requires expertise and the right analysis tools. In this article, we highlight the progress and innovation in sequencing analysis by reviewing several of the...
      05-06-2024, 07:48 AM

    ad_right_rmr

    Collapse

    News

    Collapse

    Topics Statistics Last Post
    Started by seqadmin, 05-24-2024, 07:15 AM
    0 responses
    195 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 05-23-2024, 10:28 AM
    0 responses
    218 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 05-23-2024, 07:35 AM
    0 responses
    222 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 05-22-2024, 02:06 PM
    0 responses
    12 views
    0 likes
    Last Post seqadmin  
    Working...
    X