Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • SOAPdenovo

    Hi,

    I am newbie. I am working on de novo assembly of human genome.
    I am new in the field, but not getting any help. So I would appreciate any sort of help to proceed.

    I made the DNA library, and I got my sequencing data from the sequencing facility. They ran my samples on Illumina MiSeq 2x250. This is a 250 bp PE MiSeq multiplex run. I have 4 samples, paired end reads, each has R1 and R2.

    I checked the quality by running on FastQC. I chose to run SOAP de novo I downloaded SOAP de novo assembler file : SOAPdenovo2-src-r240.tgz in my Linux, but I am not sure how to start.

    I unzip the file by the command:
    tar -zxf /home/mydir/SOAPdenovo2-src-r240.tgz

    Then, checked by
    ls -l

    and saw SOAPdenovo2-src-r240 file

    Next, I changed directory to SOAPdenovo2-src-r240 by
    cd SOAPdenovo2-src-r240

    and saw all its contents.

    Now, what would be the command to load my data file? What is the configuration file, and how do I load that?

    Please help.

    Thanks,
    Last edited by mgbfx9; 09-04-2015, 09:13 AM.

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
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
67 views
0 likes
Last Post seqadmin  
Working...
X