Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Did low input library and traditional library generated RNAseq data can be compared?

    Hello,everyone
    If there is sampleA using low input library to generate RNA-seq data
    the other one sampleB using traditional library
    Do they two sample(sampleA and sampleB) can be use to find different expression gene or other transcriptome analysis?
    Does the method of library make a bioinformatic analysis bias?
    Thanks!

  • #2
    I would be rather hesitant in comparing those, particularly if your groups are partitioned by library creation strategy. You'd be best off adding library type as a factor in your model to try and compensate for any effect.

    Comment


    • #3
      Thanks for your suggestion,but how can i do with this samples ,
      usually,i use tophat to do mapping .

      One sampe RNA only 100ng, so there no choice but low input library,the other can use traditional mehtod.

      Comment


      • #4
        If one group only has enough RNA for a low input kit, then you should use the same kit for the comparison group (ideally, use a similar amount of input). Otherwise, the output DE genes will be due to both the group-effect and a batch-effect.

        Comment


        • #5
          thanks, you are right,maybe i should think about use the same low-input library for both samples.

          Comment


          • #6
            Yeah, as a general premise, you'll always be well served by limiting uninteresting differences as much as possible. If you can't limit them, then you have to control for them, which isn't always possible (or practical).

            Comment


            • #7
              Originally posted by bioinforD View Post
              Thanks for your suggestion,but how can i do with this samples ,
              usually,i use tophat to do mapping .

              One sampe RNA only 100ng, so there no choice but low input library,the other can use traditional mehtod.
              You are aware that most current RNA-Seq protocols can easily cope with 100ng of total RNA? We regularly use the Illumina TruSeq RNA v2 protocol on 100ng and produce libraries in the 50nM range, even when dropping PCR cycle number down to 12 cycles. We've also produced library from 10ng total RNA using the NEB Ultra protocol

              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, Yesterday, 06:37 PM
              0 responses
              7 views
              0 likes
              Last Post seqadmin  
              Started by seqadmin, Yesterday, 06:07 PM
              0 responses
              7 views
              0 likes
              Last Post seqadmin  
              Started by seqadmin, 03-22-2024, 10:03 AM
              0 responses
              49 views
              0 likes
              Last Post seqadmin  
              Started by seqadmin, 03-21-2024, 07:32 AM
              0 responses
              66 views
              0 likes
              Last Post seqadmin  
              Working...
              X