Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • help with topcons membrane prediction

    Hi,

    I have been trying to use topcons membrane prediction.
    I am trying to run the consensus one, but I am stuck with

    Code:
    run_blast.sh
    of octopus.
    I am stuck at this.
    Running topcons is a 3 step process:
    1) get file from run_blast.sh
    2) process that output for modhmm profile
    3) create .mtx file

    The read_me file doesn't say clearly.
    It has instructions based on OLDER version of Blast.

    Can someone please help me with this?

    There is an other way round this:
    1) run_topcons_single.sh
    2) run_topcons.sh

    I fail to understand which one to use and how.

    I have the dependencies for TOPCONS.sh in my PATH.

    I need this prediction on standalone tools.
    I have a protein file with 35 protein sequences and I have 20 such files.

    Any help shall be greatly appreciated.
    Thank you.
    Bioinformaticscally calm

  • #2
    You get an error message? Please add more details about you problem.

    Comment


    • #3
      I get error as:

      Directory /home/robber/bin/../var/www/topcons.cbr.su.se/docroot/topcons/ does not exist

      However, the aboce directory exists in the location.
      I have added that location in my PATH as well.

      Originally posted by TiborNagy View Post
      You get an error message? Please add more details about you problem.
      Last edited by bio_informatics; 01-27-2014, 06:48 PM. Reason: Error more clear
      Bioinformaticscally calm

      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,”...
        05-24-2024, 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, 05-24-2024, 07:15 AM
      0 responses
      198 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 05-23-2024, 10:28 AM
      0 responses
      219 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 05-23-2024, 07:35 AM
      0 responses
      228 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 05-22-2024, 02:06 PM
      0 responses
      12 views
      0 likes
      Last Post seqadmin  
      Working...
      X