Create Tiled path with Gap4?

2005-10-25
2013-04-18
  • Nobody/Anonymous

    Hi all,

    Is it possible to create a tiled path with gap4. I have a dataset of bac clones and i want to create a dataset that covers the entire genome when the bacs have a minimum overlap with eachother. From all the bac clones i have the chromnumber, start and end position. Can Gap4 help me with this?

    Maarten

     
    • James Bonfield

      James Bonfield - 2005-10-27

      You probably want to investigate the Directed Assembly option. Basically create an experiment file for each sequence and then append an "AP" (assembly position) line telling gap how far away from the start of the previous sequence each sequence is. It's best to chain to the previous rather than the first otherwise gaps due to alignments can start to add up and the error rate of positioning increases.

      James

       

Get latest updates about Open Source Projects, Conferences and News.

Sign up for the SourceForge newsletter:





No, thanks