Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Analysing .ace and .bam files for SNPs

    Hi

    I have imported .ace files from 454 sequencing into both Geneious and Seqman pro. I want to find SNPs in reads and currently the analysis only highlights insertions and deletions. This is because the reads import with gaps (dashed lines) for every single variation, which means that for my ~6kb sequence I have an 18kb contig. How can I remove these gaps so that the SNP analysis works properly?

    I would appreciate any help with this!

    Thanks

  • #2
    It sounds like you are running into the issue where Newbler tends to use a deletion/insertion rather than a mismatch for a SNP. Is that a fair guess?

    Comment


    • #3
      Yes that's right. Is there no way to get around this?

      Comment


      • #4
        I've found a thread discussing this problem....

        Comment


        • #5
          That issue drove me crazy for a bit. We ended up using alternative 454 mappers for alignment, eg CLC genomics workbench, bwa-sw, or others discussed on this forum.

          Comment


          • #6
            It has been driving me crazy too! What was your experience from using alternative mappers? Have you attempted to use MIRA, which was mentioned in the other post?

            Comment


            • #7
              Originally posted by kirstyn View Post
              It has been driving me crazy too! What was your experience from using alternative mappers? Have you attempted to use MIRA, which was mentioned in the other post?
              Should do the job. Leads you on the Staden/gap5 track.
              If you are familiar with Consed, you could also use it for your mapping of 454 data (it internally uses cross_match).

              Comment


              • #8
                Otherwise novoalign should do the job pretty well, and the free version should be fast enough.
                Keep in mind they automatically trim to 160bp (or used to at least), which should be disabled for 454 reads.

                I have always had problems with bwa-sw and segmentation faults.

                Clcgenomics worked well but was very expensive.

                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