Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • MIRA Question: Improving 454 assembly with RNAseq data

    Hi All,

    I’d like to do a hybrid assembly of 454 genomic sequence and illumina RNAseq data using MIRA. Unfortunately, I’m not really sure how to do an assembly with 2 different technologies AND 2 different types of data (genomic DNA from 454 and RNA from Illumina). I’m concerned that highly expressed genes will be flagged as repetitive sequence because reads from those genes will be over-represented in the sample.

    I have a draft assembly of a bacterial genome generated with 454 reads using newbler. However, when I mapped my RNAseq data to this assembly, only a very low percentage of reads mapped back to the genome. I did this previously for a different bacterial isolate, and everything worked well (>97% of reads mapped to genome generated from assembly of 454 data). However, for this latest strain, I think there is a problem with either the coverage or the assembly, so I’d like to use as much data as possible to get a better assembly.

    Does anyone have any advice on the best way to incorporate both data types into a denovo genome assembly using MIRA?

    Thanks for all your help.

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
8 views
0 likes
Last Post seqadmin  
Started by seqadmin, Yesterday, 06:07 PM
0 responses
8 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
66 views
0 likes
Last Post seqadmin  
Working...
X