Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • search genes in a reads pool or (very) draft assembly: any usefull tool?

    Hi everyone,
    i'm in the need to screen a few bacterial genomes for the presence of around 100 genes i defined.

    We have not much sequencing data for this genomes (20MBp circa with 200bp reads), that is far from the quantity needed for a good assembly.

    I've already tryed to blastn/tblastx my genes database against reads and the contigs coming from the very draft assemblys we can get with this data but i'm not satisfied with the results because of the too high ration of false positives.

    There's a tool that can help me in this work??? maybe some kind of metagenomic tool?


    Thanks in advance to anyone that will help me

  • #2
    I haven't tried it myself, but maybe this could be of interest: http://www.plosone.org/article/info%...l.pone.0019816

    Comment


    • #3
      TBLASTX is a good way to get a lot of difficult-to-interpret noise; I strongly recommend using BLASTX against a carefully focused database of proteins. If you are concerned with false positives, tighten up your P-value cutoff.

      Merging your reads with FLASH prior to assembly may boost things a bit, if you have paired-end data. Still, depending on your bug, 20Mb of reads should be 2-10X coverage and you would be expected to get some sizable contigs. What sort of contig size distribution are you getting?

      Also, it is relevant which sequencing technology you are using. Ion's indel issue could be causing you much grief, if that is the technology.

      In the end, what is the question you wish the data to answer? It may be that this dataset is simply too sparse. On the other hand, for some questions it may well be good enough.

      Comment

      Latest Articles

      Collapse

      • 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
      • seqadmin
        Essential Discoveries and Tools in Epitranscriptomics
        by seqadmin




        The field of epigenetics has traditionally concentrated more on DNA and how changes like methylation and phosphorylation of histones impact gene expression and regulation. However, our increased understanding of RNA modifications and their importance in cellular processes has led to a rise in epitranscriptomics research. “Epitranscriptomics brings together the concepts of epigenetics and gene expression,” explained Adrien Leger, PhD, Principal Research Scientist...
        04-22-2024, 07:01 AM

      ad_right_rmr

      Collapse

      News

      Collapse

      Topics Statistics Last Post
      Started by seqadmin, 05-14-2024, 07:03 AM
      0 responses
      19 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 05-10-2024, 06:35 AM
      0 responses
      43 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 05-09-2024, 02:46 PM
      0 responses
      53 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 05-07-2024, 06:57 AM
      0 responses
      42 views
      0 likes
      Last Post seqadmin  
      Working...
      X