Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • More Unique ELAND Alignments Than Reads?

    Can anyone explain to me why I am finding more unique alignments in my eland_results file than I have reads in my sequence file?

    wc -l s7_sequence.txt
    5808194 (23232776 / 4)
    grep -c " U[0,1,2] " s7_eland_result.txt
    6371019

    It doesn't make sense to me that the uniquely aligned sequence count should be greater than the total sequences read...

    Thanks for your advice!

  • #2
    Originally posted by seq7 View Post
    Can anyone explain to me why I am finding more unique alignments in my eland_results file than I have reads in my sequence file?

    wc -l s7_sequence.txt
    5808194 (23232776 / 4)
    grep -c " U[0,1,2] " s7_eland_result.txt
    6371019

    It doesn't make sense to me that the uniquely aligned sequence count should be greater than the total sequences read...

    Thanks for your advice!
    I believe your grep is counting twice some stuff. First of all you shouldn't include a comma in square brackets, they define the alternative characters. And what does

    Code:
    wc -l s7_eland_result.txt
    output?
    Anyway, the correct grep for you is:

    Code:
    grep -cw U[012] s7_eland_result.txt
    In the end, the s_7_sequence contains the filtered and uniquely mapped reads, doesn't it? (I may be wrong, it's a long time since I've used illumina output)

    d

    Comment


    • #3
      wc -l s7_eland_result.txt
      9196920

      grep -cw U[012] s7_eland_result.txt
      6371019

      sequence.txt is filtered output.
      eland_result.txt is unfiltered ELAND alignment output.

      Thanks for the reply!

      Comment

      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
      10 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, Yesterday, 06:07 PM
      0 responses
      9 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
      67 views
      0 likes
      Last Post seqadmin  
      Working...
      X