Announcement

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

  • bait design for seqCapture

    I have questions about developing baits for sequence capture to use in population genetics of 2 very closely related species.

    We have no genomic resources for our organism (a sedge) or anything in the very large genus.

    However, we did a *very* low coverage whole genome sequencing run from our species of interest on the miSeq - we ended up with about 1/10x coverage of the genome (~250bp fragments).
    I want to use these unassembled reads to develop baits. We want to target random regions throughout the genome.

    I had never intended to assemble this data - I didn't see a need.

    After trimming, I had intended to use blast to remove as many undesirable sequences as possible (chloroplast, mitochondria, virus, bacteria, and things that blast to know repetitive DNA), and then randomly choose ~10,000 unassembled reads for bait design (designed by mycroArray/myBaits).

    However, my husband, the bioinformatics guy, thinks it is crazy to design baits from unassembled sequence.

    He thinks we need more sequence data, so we can at least partially assemble the genome before selecting regions for bait design. He argues that we can't trust unassembled reads because in a typical assembly (with more data) ~50% of reads can't be assembled, so they must be garbage - implying that from my approach 50% of the baits will be garbage.

    I realize that we could do RADseq or some variant, but prefer not to, due to possible bias (low number of individuals per locus).

    My question is whether we need to get more sequence data for a partial assembly, or if my approach is reasonable.

    Thanks for any input!

  • #2
    I think that targeting genic regions would be a better approach because they would be more conserved between or among species than intergenic region. To do this, assembly and a BLAST to identify contigs from coding region of genome is essential.

    Comment


    • #3
      thanks for your response. Yes, most people doing seqCap are using transcriptome data for bait design. But those people are interested in phylogenetics. We're interested in within-species diversity (or btw 2 very closely related species), so we don't really want conserved regions - though with 5-10,000 baits, even conserved regions would probably give enough snps to see if the 2 species are different from each other.
      My husband thinks that blasting all of the unassembled reads is unreasonable bc there are millions of reads. but metagenomics people seem to do that

      Comment

      Latest Articles

      Collapse

      • seqadmin
        Advanced Tools Transforming the Field of Cytogenomics
        by seqadmin


        At the intersection of cytogenetics and genomics lies the exciting field of cytogenomics. It focuses on studying chromosomes at a molecular scale, involving techniques that analyze either the whole genome or particular DNA sequences to examine variations in structure and behavior at the chromosomal or subchromosomal level. By integrating cytogenetic techniques with genomic analysis, researchers can effectively investigate chromosomal abnormalities related to diseases, particularly...
        Today, 06:26 AM
      • seqadmin
        How RNA-Seq is Transforming Cancer Studies
        by seqadmin



        Cancer research has been transformed through numerous molecular techniques, with RNA sequencing (RNA-seq) playing a crucial role in understanding the complexity of the disease. Maša Ivin, Ph.D., Scientific Writer at Lexogen, and Yvonne Goepel Ph.D., Product Manager at Lexogen, remarked that “The high-throughput nature of RNA-seq allows for rapid profiling and deep exploration of the transcriptome.” They emphasized its indispensable role in cancer research, aiding in biomarker...
        09-07-2023, 11:15 PM
      • seqadmin
        Methods for Investigating the Transcriptome
        by seqadmin




        Ribonucleic acid (RNA) represents a range of diverse molecules that play a crucial role in many cellular processes. From serving as a protein template to regulating genes, the complex processes involving RNA make it a focal point of study for many scientists. This article will spotlight various methods scientists have developed to investigate different RNA subtypes and the broader transcriptome.

        Whole Transcriptome RNA-seq
        Whole transcriptome sequencing...
        08-31-2023, 11:07 AM

      ad_right_rmr

      Collapse

      News

      Collapse

      Topics Statistics Last Post
      Started by seqadmin, Today, 07:53 AM
      0 responses
      7 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, Yesterday, 07:42 AM
      0 responses
      12 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 09-22-2023, 09:05 AM
      0 responses
      39 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 09-21-2023, 06:18 AM
      0 responses
      36 views
      0 likes
      Last Post seqadmin  
      Working...
      X