Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • IDBA-UD paired end data on multiple files

    I want to assemble with IDBA-UD and have no experience with it. Although my data is paired half of each pair is on one file and the other half in another with a total of 12 files (~22Gb in total). Looking around online it didn't seem as if anyone had this issue before. I was also wondering if there is a way to set the K-mer as 35 instead of having to set the mink and maxk? Any help would be greatly appreciated.

    Tom

  • #2
    For paired end reads, the R1 and R2 from each pair are usually in separate files.

    Comment


    • #3
      Ok thanks, first time using this data so was unsure. Any idea how to upload them to IDBA-UD for assembly?

      Comment


      • #4
        Anyone know? All help is appreciated.

        Comment


        • #5
          I have not used IDBA-UD.

          If you have IDBA-UD installed on your computer, there is a README file in the IDBA directory, that tells you how to pre-process your data for input to IDBA. I think you need to convert fastq files to fasta, and have paired reads together in the same file. They give examples of how to do this using scripts included with IDBA.

          The website gives examples of parameters used with their test datasets.

          Comment

          Latest Articles

          Collapse

          • seqadmin
            Latest Developments in Precision Medicine
            by seqadmin



            Technological advances have led to drastic improvements in the field of precision medicine, enabling more personalized approaches to treatment. This article explores four leading groups that are overcoming many of the challenges of genomic profiling and precision medicine through their innovative platforms and technologies.

            Somatic Genomics
            “We have such a tremendous amount of genetic diversity that exists within each of us, and not just between us as individuals,”...
            Yesterday, 01:16 PM
          • 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

          ad_right_rmr

          Collapse

          News

          Collapse

          Topics Statistics Last Post
          Started by seqadmin, Yesterday, 07:15 AM
          0 responses
          12 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 05-23-2024, 10:28 AM
          0 responses
          15 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 05-23-2024, 07:35 AM
          0 responses
          16 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 05-22-2024, 02:06 PM
          0 responses
          9 views
          0 likes
          Last Post seqadmin  
          Working...
          X