Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • split the abacas joined chromosomes

    Hi, All. I just tried to align my contigs to a genome which has 9 chromosomes using ABACAS. I followed the PAGIT toolkit published on nature protocol, but after I joined the chromosomes together as required by abacas, I could not split the files, the script in the PAGIT "split2multifasta.pl did not work. Does some one have suggestions? Thank you.
    yun

  • #2
    Originally posted by yzzhang View Post
    Hi, All. I just tried to align my contigs to a genome which has 9 chromosomes using ABACAS. I followed the PAGIT toolkit published on nature protocol, but after I joined the chromosomes together as required by abacas, I could not split the files, the script in the PAGIT "split2multifasta.pl did not work. Does some one have suggestions? Thank you.
    yun
    Can you provide details about the statement "PAGIT split2multifasta.pl did not work" ?

    Comment


    • #3
      I looked through the split2multifasta.pl script, there were only few lines like that
      use strict;


      if (scalar(@ARGV)<5) {
      die "usage: <Reference File> <ordered ABACAS query file> <resultName> <crunchfile> <Tag>\n\nThis script will split the query file accordinly to the reference, assuming the reference got processed with joinMultifasta.pl.\n";
      }

      my $spacer;
      my $splitinfo = shift;
      my $queryFile = shift;
      my $crunchFile = shift;
      my $resultName = shift;

      print "Sorry, this script has not yet be included properly to the PAGIT distribution.\n";
      .I email the author, and he kindly sent me the script and now I can use this pipeline now.

      Comment


      • #4
        Has anyone had any trouble running this script? When I try to run it nothing happens. I don't get any errors it just seems to sit there and produce nothing. Does it take a long time to run?

        Thanks

        Comment

        Latest Articles

        Collapse

        • 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
        • 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

        ad_right_rmr

        Collapse

        News

        Collapse

        Topics Statistics Last Post
        Started by seqadmin, 05-14-2024, 07:03 AM
        0 responses
        19 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 05-10-2024, 06:35 AM
        0 responses
        44 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 05-09-2024, 02:46 PM
        0 responses
        54 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 05-07-2024, 06:57 AM
        0 responses
        42 views
        0 likes
        Last Post seqadmin  
        Working...
        X