Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Number of Reads in 454 Library

    What's the average/range of the total number of reads in 454 library?

  • #2
    The number will depend on the type of chemistry, the number of regions you are using (e.g., whole plate, quads, etc.), loss of quality that you willing to tolerate within the sequencing, the quality of your starting material, etc.

    Just to throw out some numbers our last titanium run with 4 different experiments (samples) on it gave us:

    136538 reads at 553 bases with std. deviation of 332 bases.
    392301 reads at 298 std. dev. 137 bases
    369737 reads at 318 std. dev. 154 bases
    391092 reads at 325 std. dev. 154 bases

    So roughly 1.3 million reads of around 300 bases or ~400 M base pairs.

    Comment


    • #3
      I really depends a lot on what you're doing. Our first run with a bacteria on the titanium got 1,371,195 reads, avg 397.4, std. dev. 135. In total 505Mb.
      But now we're doing runs with array enrichment and we get about 100Mb less per run. Although I've been told that a new protocol for array enrichment will perform much better.

      Comment


      • #4
        Which enrichment system are you using? I was thinking of using Nimblegen, but it seams too expensive, so I am starting with some test with the Combimatrix array first. Anyone using Combimatrix for seq enrichemnt??

        Comment


        • #5
          We're using the Nimblegen enrichment. We're doing the enrichment in-house so that makes it a lot cheaper.

          Comment


          • #6
            I was thinking of doing the same thing, but my concern is if it is possible to tag the samples before doing the enrichment. My target is <<5Mb, so I was thinking of using the Nimblegen array with a high tilling (many copies of the same few probes targeting 100kb per sample) so that I could enrich many samples all together.
            I was wondering if you ever tried anything like that?

            Comment

            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, Today, 07:24 AM
            0 responses
            9 views
            0 likes
            Last Post seqadmin  
            Started by seqadmin, Yesterday, 08:58 AM
            0 responses
            11 views
            0 likes
            Last Post seqadmin  
            Started by seqadmin, 06-12-2024, 02:20 PM
            0 responses
            15 views
            0 likes
            Last Post seqadmin  
            Started by seqadmin, 06-07-2024, 06:58 AM
            0 responses
            182 views
            0 likes
            Last Post seqadmin  
            Working...
            X