Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • konrad98
    replied
    Under the contrib/extractContigReads directory in Velvet you'll find a script to do this

    Leave a comment:


  • choy
    replied
    Velvet question

    How can one extract all of the reads that were used in the assembly, in order to do the re-mapping step you described?

    Leave a comment:


  • konrad98
    replied
    Hi Simon,

    I'm not by any means an expert on this, but you probably have two options:

    1. Convert the kmer coverage in the stats.txt file to base-coverage and use that as a proxy for expression level

    2. Align the reads to the assembled transcripts using something like Bowtie and then extract the coverage of each transcript using SAMTools

    Hope that helps!

    Leave a comment:


  • Velvet/Oases transcript expression level?

    Hi,
    I am in the process of de novo transcriptome assembly from a non-model eukaryote. I have 17 million 65 bp, paired-end reads that I have assembled with Velvet and then Oases. This gives nice results in that I am getting full-length contigs that appear reasonable when compared to orthologues in related model eukaryotes. However, I am really after relative transcript expression levels. Does anyone know if there as a way that I can get information on that from this software combination?

Latest Articles

Collapse

  • seqadmin
    Current Approaches to Protein Sequencing
    by seqadmin


    Proteins are often described as the workhorses of the cell, and identifying their sequences is key to understanding their role in biological processes and disease. Currently, the most common technique used to determine protein sequences is mass spectrometry. While still a valuable tool, mass spectrometry faces several limitations and requires a highly experienced scientist familiar with the equipment to operate it. Additionally, other proteomic methods, like affinity assays, are constrained...
    04-04-2024, 04:25 PM
  • 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

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by seqadmin, 04-11-2024, 12:08 PM
0 responses
13 views
0 likes
Last Post seqadmin  
Started by seqadmin, 04-10-2024, 10:19 PM
0 responses
19 views
0 likes
Last Post seqadmin  
Started by seqadmin, 04-10-2024, 09:21 AM
0 responses
16 views
0 likes
Last Post seqadmin  
Started by seqadmin, 04-04-2024, 09:00 AM
0 responses
43 views
0 likes
Last Post seqadmin  
Working...
X