Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Hisat2: no command found in bash

    Hi all,
    I'm a complete novice at RNAseq mapping and I am trying to follow this protocol using their data: https://www.nature.com/nprot/journal...t.2016.095.pdf

    I have downloaded the appropriate files and unpacked them and copied the relevant files into my working directory (HOME/bin) but when I try to run the first command to map the reads to the genome ($ hisat2 -p 8 --dta -x chrX_data/indexes/chrX_tran -1) bash spits out the following error: -bash: hisat2: command not found

    The hisat2 executable file in present in my working directory, so I can't understand why it won't run.
    Any advice would be much appreciated as my boss is back next week and I would like to have made some progress by then. I've been struggling with this since yesterday and can't seem to get past it.

    Thank you in advance.
    Samantha

  • #2
    While you would be able to get the command to run by doing
    Code:
    $ ./hisat2 -p 8 --dta -x chrX_data/indexes/chrX_tran -1 etc
    you should spend a bit of time with some unix basics. I recommend this UNIX tutorial.

    Comment


    • #3
      Problem solved!

      Thank you so much GenoMax!! This advice worked a treat!

      I will definitely take the time to learn the basics, and hopefully beyond! Thanks for the tutorial link.

      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