Unconfigured Ad

Collapse
X
 
  • Time
  • Show
Clear All
new posts
  • analyst
    Member
    • Jan 2011
    • 18

    #1

    Bowtie behavior with --best

    ok, i apologize it may be just something very obvious but despite reading manual several times, i can not understand the following behavior. A sequence searched against build in e_coli index:

    bowtie e_coli -c TTCTTTTTTACCTTCCCC -n 3 -e 90 -a
    0 + gi|110640213|ref|NC_008253.1| 2745489 TTCTTTTTTACCTTCCCC IIIIIIIIIIIIIIIIII 0
    0 - gi|110640213|ref|NC_008253.1| 3948415 GGGGAAGGTAAAAAAGAA IIIIIIIIIIIIIIIIII 0 9:C>T,10:T>G,12:G>A
    0 + gi|110640213|ref|NC_008253.1| 2345717 TTCTTTTTTACCTTCCCC IIIIIIIIIIIIIIIIII 0 13:G>T,16:T>C,17:G>C
    0 + gi|110640213|ref|NC_008253.1| 1032847 TTCTTTTTTACCTTCCCC IIIIIIIIIIIIIIIIII 0 11:G>C,13:A>T,16:G>C
    0 + gi|110640213|ref|NC_008253.1| 2899814 TTCTTTTTTACCTTCCCC IIIIIIIIIIIIIIIIII 0 11:T>C,15:A>C
    0 + gi|110640213|ref|NC_008253.1| 2939803 TTCTTTTTTACCTTCCCC IIIIIIIIIIIIIIIIII 0 9:C>A,10:A>C,15:G>C
    0 + gi|110640213|ref|NC_008253.1| 550112 TTCTTTTTTACCTTCCCC IIIIIIIIIIIIIIIIII 0 0:G>T,1:C>T
    0 + gi|110640213|ref|NC_008253.1| 4879006 TTCTTTTTTACCTTCCCC IIIIIIIIIIIIIIIIII 0 8:C>T,13:G>T,15:T>C
    0 + gi|110640213|ref|NC_008253.1| 4630520 TTCTTTTTTACCTTCCCC IIIIIIIIIIIIIIIIII 0 8:G>T,12:A>T,14:G>C
    # reads processed: 1
    # reads with at least one reported alignment: 1 (100.00%)
    # reads that failed to align: 0 (0.00%)
    Reported 9 alignments to 1 output stream(s)

    =========================================================

    bowtie e_coli -c TTCTTTTTTACCTTCCCC -n 3 -e 90 -a --best
    0 + gi|110640213|ref|NC_008253.1| 2745489 TTCTTTTTTACCTTCCCC IIIIIIIIIIIIIIIIII 0
    0 + gi|110640213|ref|NC_008253.1| 550112 TTCTTTTTTACCTTCCCC IIIIIIIIIIIIIIIIII 0 0:G>T,1:C>T
    0 + gi|110640213|ref|NC_008253.1| 2899814 TTCTTTTTTACCTTCCCC IIIIIIIIIIIIIIIIII 0 11:T>C,15:A>C
    0 + gi|110640213|ref|NC_008253.1| 4760194 TTCTTTTTTACCTTCCCC IIIIIIIIIIIIIIIIII 0 0:A>T,2:A>C,14:A>C
    0 + gi|110640213|ref|NC_008253.1| 2345717 TTCTTTTTTACCTTCCCC IIIIIIIIIIIIIIIIII 0 13:G>T,16:T>C,17:G>C
    # reads processed: 1
    # reads with at least one reported alignment: 1 (100.00%)
    # reads that failed to align: 0 (0.00%)
    Reported 5 alignments to 1 output stream(s)

    =========================================================

    Q.1 what happened to other 4 alignments with best (no quality is considered as you see)
    Q.2 Where is the alignment 4760194 coming from when --best is used

    Thanks for your response
    Last edited by analyst; 05-05-2011, 06:10 AM.

Latest Articles

Collapse

  • SEQadmin2
    Multiomic Liquid Biopsy: What DNA/RNA Panels Reveal That DNA Alone Can’t
    by SEQadmin2



    Tumors contain complex mixtures of cell populations that evolve in response to treatment and host-specific factors. Tissue biopsies provide only static snapshots of a tumor’s state. But what if we could follow that evolution over time using a minimally invasive technique?

    Liquid biopsies can detect tumor-derived material circulating in the bloodstream, providing a way to study treatment response, detect emerging resistance, and discover new biomarkers. Circulating
    ...
    10-14-2026, 09:55 AM
  • SEQadmin2
    New Genomics Technologies Take Aim at Long-Standing Limits
    by SEQadmin2


    Researchers using sequencing and genomics tools often have to make trade-offs. They can choose between speed or scale, short reads or long-range information, or targeted panels or a view of the whole transcriptome. New technologies that have been released this year are built to address those tough choices.

    We asked six companies the same four questions to learn about their latest products. The new technologies bring a lot to the table, including rethinking sequencing
    ...
    09-28-2026, 10:25 AM

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by SEQadmin2, Yesterday, 11:13 AM
0 responses
19 views
0 reactions
Last Post SEQadmin2  
Started by SEQadmin2, Yesterday, 10:48 AM
0 responses
18 views
0 reactions
Last Post SEQadmin2  
Started by SEQadmin2, 10-15-2026, 10:52 AM
0 responses
36 views
0 reactions
Last Post SEQadmin2  
Started by SEQadmin2, 10-14-2026, 05:39 AM
0 responses
42 views
0 reactions
Last Post SEQadmin2  
Working...