Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Claudia Stewart
    replied
    Has anyone seen a very high percentage of dots whenlooking at tandem repeats (80%)? Can you adjust the reaction to read through these and/or capture the data back from the filter to analyse what is really going on?

    Leave a comment:


  • pmiguel
    replied
    Originally posted by Melissa View Post
    Agree with westermann. I'm sure you know the location of that repeat. Just design primers flanking that region and amplify it. Forward and reverse sequencing using Sanger should do the job. After all, it's just 1kb!!!!
    Probably won't work. If these are identical short tandem repeats there is no basis to align the forward and reverse reads.

    Phillip

    Leave a comment:


  • Melissa
    replied
    Agree with westermann. I'm sure you know the location of that repeat. Just design primers flanking that region and amplify it. Forward and reverse sequencing using Sanger should do the job. After all, it's just 1kb!!!!

    Leave a comment:


  • westerman
    replied
    You might be able to get a 3730 to sequence over 1000 bases. We have had a couple hundred 1000+ base high quality base sequencing runs (out of thousands) over the last 10 years. Bribe your friendly sequencing center to take extra care in the sequencing run. It does depend on if your sequence has homopolymer segments within the repeats.

    I agree that you won't be able to get this information from a 2nd gen system.

    Leave a comment:


  • nickloman
    replied
    Sounds like you have 11 or so tandem perfect repeats each 90 base pairs.

    How many times do these regions occur in your genome?

    If only once, you could try and use read depth (as mapped against a single copy of the repeat, or a repetitive contig as produced by Newbler) as a guide to the total number of copies.

    Otherwise I think you will have difficulty using your existing data to get an answer as your repeats are longer than read length.

    Leave a comment:


  • gaster
    replied
    Thanks for your reply. We think these are perfect repeats of 90 basepairs. It is just one region so we would rather not do another 454 or a Solexa run. Any ideas?

    Leave a comment:


  • nickloman
    replied
    Originally posted by gaster View Post
    Anyone know of a way to sequence repeats? We have a large 1000bp region of repeats. We can't sequence though it with either 454 or even ABI. Seems like there might some techniques out there for this?

    Anyone?

    Thanks,

    Gaster
    Tricky - you need to define a bit more clearly the nature and structure of the repeats (are they likely to be perfect, imperfect, tandem or separated, is the repeat 1000bp long or is it a kilobase of shorter repeats?). Paired-end reads are often helpful for repeat regions I believe 454 can use 3kb and 20kb inserts and Illumina offer short (250-500bp) and mid-range (2-5kb) inserts. But despite all this, some kinds of repeats are still 'impossible' to sequence.

    Leave a comment:


  • gaster
    started a topic Sequencing repeats: how to?

    Sequencing repeats: how to?

    Anyone know of a way to sequence repeats? We have a large 1000bp region of repeats. We can't sequence though it with either 454 or even ABI. Seems like there might some techniques out there for this?

    Anyone?

    Thanks,

    Gaster

Latest Articles

Collapse

  • seqadmin
    Best Practices for Single-Cell Sequencing Analysis
    by seqadmin



    While isolating and preparing single cells for sequencing was historically the bottleneck, recent technological advancements have shifted the challenge to data analysis. This highlights the rapidly evolving nature of single-cell sequencing. The inherent complexity of single-cell analysis has intensified with the surge in data volume and the incorporation of diverse and more complex datasets. This article explores the challenges in analysis, examines common pitfalls, offers...
    06-06-2024, 07:15 AM
  • seqadmin
    Latest Developments in Precision Medicine
    by seqadmin



    Technological advances have led to drastic improvements in the field of precision medicine, enabling more personalized approaches to treatment. This article explores four leading groups that are overcoming many of the challenges of genomic profiling and precision medicine through their innovative platforms and technologies.

    Somatic Genomics
    “We have such a tremendous amount of genetic diversity that exists within each of us, and not just between us as individuals,”...
    05-24-2024, 01:16 PM

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by seqadmin, Yesterday, 07:24 AM
0 responses
10 views
0 likes
Last Post seqadmin  
Started by seqadmin, 06-13-2024, 08:58 AM
0 responses
11 views
0 likes
Last Post seqadmin  
Started by seqadmin, 06-12-2024, 02:20 PM
0 responses
16 views
0 likes
Last Post seqadmin  
Started by seqadmin, 06-07-2024, 06:58 AM
0 responses
184 views
0 likes
Last Post seqadmin  
Working...
X