Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Clipping and trimming with MrFast (for eventual CNV discovery)

    In the mrFAST manual, it says:

    NOTE: mrFAST will assume that the read lengths are uniform within a file (paired-ends may differ from each other). If the lengths of the reads are not the same in a file, it may crash or output incorrectly formatted SAM files.
    Since my sequencing pipelines trims and clips the fastq files by using the fastq-mcf utility, the sequences will not be completely uniform in length. I was wondering if MrFast only worked on raw, untrimmed and unclipped data, or if this particular pre-processing step was acceptable for use with mrFAST.

  • #2
    So to anyone who might still be interested. After some testing, I did get a Segmentation fault when using trimmed/clipped reads. Thus, I considered two different options.

    1. Use the clip/trim data, but remove additional bases at the end of reads to make the length uniform (and discard the reads that are too short for this process).

    2. Use the raw reads.

    I chose to use the raw reads, since for CNV calling the low quality bases at the end of the sequences shouldn't be too problematic. Also, I figured the mapping quality shouldn't be affected in a very significant manner.

    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
    198 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 05-23-2024, 10:28 AM
    0 responses
    220 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 05-23-2024, 07:35 AM
    0 responses
    229 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 05-22-2024, 02:06 PM
    0 responses
    13 views
    0 likes
    Last Post seqadmin  
    Working...
    X