Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • How many multiple alignments to allow?

    Hi everyone, I am working with human transcriptome sequenced by SOLiD - at the moment single read, but plan to try mate paired next - and using Bowtie/TopHat/Cufflinks to align reads. I am fairly new here and I have a simple but very important question.

    How many multiple alignments should you allow for each read?

    Its a difficult question when a read will map equally well to more than one location (how do you call which is best?). As I understand it TopHat, as default, reports up to 40 different alignments per read. I know this can be adjusted using the -max-multihits option, but this gets rid of every alignment for reads mapping at multiple sites. Bowtie has options for --best --strata but this still reports all reads which are best (at least when I run the command it does). There are also options for -k, -a, -m, -M.

    How am I supposed to know or choose which option(s) to apply to my data? Surely if I allow the software to report all possible mappings then I am biasing my data for later stages when RPKM is calculated?

    I just wondered what the wider community was doing about this, and what sort of parameters you are applying to your data?

    Many thanks
    Helen

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