Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • dpryan
    replied
    I've noticed that happen on occasion and still haven't really found the cause. My presumption is that the random seeding will be slightly different if you split the files (if the random number generator is always given the same seed, then splitting up a file will result in different numbers being produced if you split reads over files, as opposed to the completely reproducible results if you run an alignment twice). Interestingly, apparently a similar thing happens in BWA if you use different numbers of threads. This was discussed over on Biostars and no one's come up with the base cause yet.

    Leave a comment:


  • Tonnny97
    started a topic Try to further accelerate Bowtie2 alignment

    Try to further accelerate Bowtie2 alignment

    Hi all,

    I try to further accelerate Bowtie2 alignment by separating input file to several pieces and using Hadoop-like computing framework to execute.
    Based on my understanding, Bowtie2 aligns each pair of read independently.
    However, when I separate input files into two parts and merge two outputs of Bowtie2, the content of result file is somewhat not consistent with that of result file generated without separating input.

    I would like to ask whether Bowtie2 has some dependent task inside?
    Does separating files and then merging the output make sense in Bowtie2?
    Thanks.
    Last edited by Tonnny97; 01-19-2014, 05:15 PM.

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