Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Which format of reads quality is assumed in bfast bwaaln command

    Hello,

    I am using bfast to align reads (paired-end) from Illumina GAIIx, so the first step is to perform the bfast bwaaln command. I am wondering whether this command assumes that the quality of the reads are Illumina 1.3+ or not, since the -I argument that bwa has to indicate so is not availaible in bfast (or at least, in the bfast+bwa-0.6.4e i am currently using).

    By the way, how can I know the version of the BWA used by a certain bfast+bwa release?

    Thanks a lot!
    David

  • #2
    Originally posted by david.tamborero View Post
    Hello,

    I am using bfast to align reads (paired-end) from Illumina GAIIx, so the first step is to perform the bfast bwaaln command. I am wondering whether this command assumes that the quality of the reads are Illumina 1.3+ or not, since the -I argument that bwa has to indicate so is not availaible in bfast (or at least, in the bfast+bwa-0.6.4e i am currently using).
    The aim is not to integrate BWA fully into BFAST, but to use BWA (short) to map very short sequences, for example when SOLiD first came out with its paired end kit (50+25), and we wanted to sensitively map the 25bp portion.

    Therefore, unless you have short data (less than 35bp), use "bfast match".

    By the way, how can I know the version of the BWA used by a certain bfast+bwa release?
    Again, no version, as it this functionality is not meant to replicate BWA.

    Comment


    • #3
      I totally missed that point, sorry for that.

      But anyway, regardless of bfast bwaalign or bfast match, the alignement process should take into account the qualities of the reads at some step(s). So still, if they are Illumina (-A 0), how it is known the quality format (for instance, 1.3+ or 1.5+)? It is automatically detected?

      Thnks again for your time,

      cheers
      david

      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, 03-27-2024, 06:37 PM
      0 responses
      12 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 03-27-2024, 06:07 PM
      0 responses
      11 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 03-22-2024, 10:03 AM
      0 responses
      53 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 03-21-2024, 07:32 AM
      0 responses
      68 views
      0 likes
      Last Post seqadmin  
      Working...
      X