Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • PINDEL -c (chromosome) flag for multiple chromosomes

    Hi all,

    I was wondering whether I can use -c flag in pindel for multiple chromosomes but not ALL. For example: is it possible to choose only chromosome 11 and 20 rather than all chromosomes or NOT running for each chromosome individually?

    Thanks in advance.

    Regards
    Last edited by opulcy97; 05-14-2013, 07:00 AM.

  • #2
    Originally posted by opulcy97 View Post
    Hi all,

    I was wondering whether I can use -c flag in pindel for multiple chromosomes but not ALL. For example: is it possible to choose only chromosome 11 and 20 rather than all chromosomes or NOT running for each chromosome individually?

    Thanks in advance.

    Regards
    hi,

    I am implementing a bed input option. with -j, you can specify which regions to include and with -J which to exclude. half way already. please check out the code (genome/pindel at github) be the end of next week.

    Kai

    Comment


    • #3
      Yesterday committed changes to github genome/pindel (https://github.com/genome/pindel). Now -j (include) and -J (exclude) options are available.

      Now you can use -c, -j and -J to specify the region of interest/exclude. Pindel first takes -c, -j and -J regions to find out what genomic regions for current run (print the list of regions to screen), then go through each region one by one.

      Please let me know whether this is what you needed and do notify me if you find anything strange.

      kai

      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
      10 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, Yesterday, 06:07 PM
      0 responses
      9 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 03-22-2024, 10:03 AM
      0 responses
      49 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 03-21-2024, 07:32 AM
      0 responses
      67 views
      0 likes
      Last Post seqadmin  
      Working...
      X