Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • RCJK
    replied
    How about Newbler for the 454 reads? Not sure how it would deal w/ PacBio data, but if you use fasta + qual I think it could handle it (depending on read length).

    Leave a comment:


  • ulz_peter
    replied
    I guess it depends on how many reads you've got. For a moderate number of seuqences BLAT does a good job as well.
    I used bwasw for 454 data as well and it worked out nicely.

    Leave a comment:


  • Protaeus
    started a topic 454: Extremely general question

    454: Extremely general question

    All,

    I have 454 and PacBio SRA data (that are cleaned of adaptors) that I'd like to align to a reference. I've tried bwasw, but when I look at the alignments in samtools tview, they are rather subpar as compared to data that has been reported by others on these sequences. Any suggestions for general approaches to aligning long reads? bwasw should work, correct? Better tools for dealing with these data?

Latest Articles

Collapse

  • seqadmin
    Exploring the Dynamics of the Tumor Microenvironment
    by seqadmin




    The complexity of cancer is clearly demonstrated in the diverse ecosystem of the tumor microenvironment (TME). The TME is made up of numerous cell types and its development begins with the changes that happen during oncogenesis. “Genomic mutations, copy number changes, epigenetic alterations, and alternative gene expression occur to varying degrees within the affected tumor cells,” explained Andrea O’Hara, Ph.D., Strategic Technical Specialist at Azenta. “As...
    07-08-2024, 03:19 PM
  • seqadmin
    Exploring Human Diversity Through Large-Scale Omics
    by seqadmin


    In 2003, researchers from the Human Genome Project (HGP) announced the most comprehensive genome to date1. Although the genome wasn’t fully completed until nearly 20 years later2, numerous large-scale projects, such as the International HapMap Project and 1000 Genomes Project, continued the HGP's work, capturing extensive variation and genomic diversity within humans. Recently, newer initiatives have significantly increased in scale and expanded beyond genomics, offering a more detailed...
    06-25-2024, 06:43 AM

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by seqadmin, 07-19-2024, 07:20 AM
0 responses
29 views
0 likes
Last Post seqadmin  
Started by seqadmin, 07-16-2024, 05:49 AM
0 responses
42 views
0 likes
Last Post seqadmin  
Started by seqadmin, 07-15-2024, 06:53 AM
0 responses
50 views
0 likes
Last Post seqadmin  
Started by seqadmin, 07-10-2024, 07:30 AM
0 responses
43 views
0 likes
Last Post seqadmin  
Working...
X