Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • question about hisat2

    I want to use hisat2. According to the manual, "Use extract_splice_sites.py (in the HISAT2 package) to extract splice sites from a GTF file", I do it as:
    bac@bac-X10DAi:~/hisat2-2.0.0-beta$ python extract_splice_sites.py mus.gtf > s.txt

    the mus.gtf is in the hisat2-2.0.0-beta folder, but the output s.txt is empty!!!

    I do not know where is wrong???

  • #2
    Are there any other errors? Does mus.gtf have content (i.e. it is not empty)?

    Comment


    • #3
      Originally posted by GenoMax View Post
      Are there any other errors? Does mus.gtf have content (i.e. it is not empty)?
      You are right, it seems the mus.gtf lack something. I just download this gtf file from ensembl at random. I try other gtf files, they are all ok!

      But I found an another problem. When I run hisat2-build to index the genome, if I add --ss and --exons parameters, it can not finish with an error "illlegal instruction (core dump)". Is this due to insufficient memory? If I don't add these parameters, it is ok.

      Also, I want to know whether adding "--ss" and "--exon" will give us a better result? Is these parameter like -G xx.gtf in tophat? and let the software map reads to transcripts first?

      Comment


      • #4
        You have to put the --ss and --exon parameters, and --large-index if needed or desired, after the path to your genome sequence even though the online manual and command line help has them before it. Like this:

        hisat2-build -p 16 Triticum_aestivum.IWGSC1.0+popseq.29.dna.genome.fa --large-index --ss wheat_splice_sites.txt --exon wheat_exons.txt Triticum_aestivum

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