Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Is Data filtering step mandatory?

    Hi All,

    I have been trying to use Tophat and also RSEM on illumina data. I always filter the data first when I use Tophat and I have always wondered whether it does its own filteration step or it would be better to filter the data yourself and then trim it using FASTX toolkit etc. Using this approach and then using cuffdiff the overlap with qrtpcr has not been good. So I started using RSEM and I thought I made a mistake by not filtering the reads but then I found that RSEM does neglects the reads by itself as is evident from its output.

    # reads processed: 54476831
    # reads with at least one reported alignment: 45346199 (83.24%)
    # reads that failed to align: 9054059 (16.62%)
    # reads with alignments suppressed due to -m: 76573 (0.14%)

    Thus I was wondering whether my analysis with RSEM would be correct or wrong. As ideally such tools should automatically filter the reads if they are not bad.

  • #2
    It's not clear to me what you mean by filtering; do you mean trimming off low-quality bases and dropping short/N-containing reads, or something else?

    You might want to know what those 16 % non-mapped reads are - if they contain adapter sequences it is lost data that could possibly be recovered.
    It is not really necessary to trim off low quality 3' ends with RSEM, since it allows for many mismatches outside Bowtie's seed region (unless they've changed that recently). However, I'd clip off adapter sequences (if any suspected when examining the data with e.g. FastQC) and remove rRNA reads to avoid total read count biases (rRNA tend to be abundant and sometimes at quite different amounts in different samples).

    Comment

    Latest Articles

    Collapse

    • seqadmin
      Strategies for Sequencing Challenging Samples
      by seqadmin


      Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...
      03-22-2024, 06:39 AM
    • seqadmin
      Techniques and Challenges in Conservation Genomics
      by seqadmin



      The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.

      Avian Conservation
      Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...
      03-08-2024, 10:41 AM

    ad_right_rmr

    Collapse

    News

    Collapse

    Topics Statistics Last Post
    Started by seqadmin, Yesterday, 06:37 PM
    0 responses
    11 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, Yesterday, 06:07 PM
    0 responses
    10 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 03-22-2024, 10:03 AM
    0 responses
    51 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 03-21-2024, 07:32 AM
    0 responses
    68 views
    0 likes
    Last Post seqadmin  
    Working...
    X