Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Trinity contig filtering

    Hello, all,

    I have just got my Trinity assembly, the N50 looks good. However, I have 100 contigs length extends from 4000bp to 11700bp.
    Because we don't expect the contig size to be above 4000bp, so is this because of some genomic contaimination?
    And can anyone suggest a program or script that can filter out the bad contigs? Thanks a lot,

  • #2
    I'm not sure what those contigs would be. Maybe chimeras? Have you tried blasting them?

    If you're just looking to get rid of all sequences over 'x' length, then you can do something like below (if you have bioPerl installed). Usage: perl script.pl --in startingfile.fas --cutoff 4000 --out prunedfile.fas


    Code:
    #!/usr/bin/perl
    
    use strict;
    use warnings;
    use Getopt::Long;
    use Bio::SeqIO;
    
    my $inFile;
    my $cutoff;
    my $outFile;
    
    GetOptions  ("in=s"      => \$inFile,
                 "cutoff=i"  => \$cutoff,
                 "out=s"     => \$outFile) || die "Couldn't get parameters with Getopt::Long.\n";
    
    my $seqIn = Bio::SeqIO->new(-file   => $inFile,
                                -format => 'fasta');
    my $seqOut = Bio::SeqIO->new(-file   => ">$outFile",
                                 -format => 'fasta');
    
    while (my $seq = $seqIn->next_seq()) {
        if ($seq->length() < $cutoff) {
            $seqOut->write_seq($seq);
        }
    }
    Last edited by atcghelix; 10-10-2013, 09:30 PM. Reason: Mention that you need bioPerl for this to run.

    Comment


    • #3
      Thanks, it helps

      Comment


      • #4
        Originally posted by ripeapple View Post
        Hello, all,

        I have just got my Trinity assembly, the N50 looks good. However, I have 100 contigs length extends from 4000bp to 11700bp.
        Because we don't expect the contig size to be above 4000bp, so is this because of some genomic contaimination?
        And can anyone suggest a program or script that can filter out the bad contigs? Thanks a lot,
        Its possible its prespliced or incompletely spliced RNAs. However, why do you assume you shouldn't have >4000bp contigs? Ttn is >100,000bp. So certainly there are genes this big.

        Also, have you tried Trinity's downstream analysis modules. They are very good at picking out protein coding orfs and blasting your dataset to identify orthologs

        Comment


        • #5
          Yes, you're right,
          I was thinking to remove the possible genomic contamination at first to set a cutoff for contig size.
          Now I guess I need to map the sequence back to assembly see how it goes,
          Thanks,

          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, 03-27-2024, 06:37 PM
          0 responses
          13 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 03-27-2024, 06:07 PM
          0 responses
          11 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 03-22-2024, 10:03 AM
          0 responses
          53 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 03-21-2024, 07:32 AM
          0 responses
          69 views
          0 likes
          Last Post seqadmin  
          Working...
          X