Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • which is better, paired or single end

    Can anyone please answer these

    For chip-seq and RNA-seq, which is better PE or SE

    In one lane in illumina, one gets ~15 GB sequence which is 5X for human. Is this enough for chip-seq and RNA seq, or should one run multiple lanes.

    Is it good idea to multiplex in the above experiment if budget is constraint.

    Thanks in advance for you valuable time. It will be a big help really.

  • #2
    PE is almost always better for RNA-seq--you gain more information about splice junctions etc. It doesn't hurt for ChIP-Seq and may help you better identify enriched binding sites in repetitive regions (although some mappers may not be able to handle PE tags).

    For most ChIP-Seq applications 10-15 million reads is enough (unless it's a histone or highly ubiquitous TF). You can computationally determine your ChIP-Seq coverage/saturation using a program like MACS --diag option. I can't say much for RNA-Seq but somewhere out there I've seen a table with suggested sequence coverage. RNA-Seq probably requires more reads than ChIP-Seq, moreso if you plan on getting quantitative information out of it.

    Comment


    • #3
      PE for RNA Seq
      SE for ChIP Seq. There really isn't the need for Paired reads.

      the throughput really varies on the experiment. Histone modifications or TF analysis?

      Comment


      • #4
        SE is better for you .

        Comment


        • #5
          SE is faster and cheaper... PE on the other hand is more data, and theoretically more efficient, provided you use the appropriate methods to make use of paired information
          --
          bioinfosm

          Comment


          • #6
            Actually, I would suggest using PE for ChIP-seq too. For SE reads, existing ChIP-seq software, such as MACS, shift and extend the reads to build the whole genome profile. The shift and extend distance was a fixed value estimated from the double peak pattern or provided by command line parameters. This might be inaccurate if the wrong shift/extend distance were used, and might cause the peak appear as doublets. So the peak heights are sensitive to the shift/extend values. PE sequencing provides fragment size information, therefore build whole genome profile is straightforward, no shift or extend involved. PE is also not that expensive compared with SE.

            Originally posted by SeqAA View Post
            PE for RNA Seq
            SE for ChIP Seq. There really isn't the need for Paired reads.

            the throughput really varies on the experiment. Histone modifications or TF analysis?
            Last edited by yxibcm; 10-05-2011, 11:34 AM.

            Comment


            • #7
              Are there peak callers that accept paired-end data?
              --------------
              Ethan

              Comment


              • #8
                A little searching answers that question:

                Background ChIP-Seq, which combines chromatin immunoprecipitation (ChIP) with high-throughput massively parallel sequencing, is increasingly being used for identification of protein-DNA interactions in vivo in the genome. However, to maximize the effectiveness of data analysis of such sequences requires the development of new algorithms that are able to accurately predict DNA-protein binding sites. Results Here, we present SIPeS (S ite I dentification from P aired-e nd S equencing), a novel algorithm for precise identification of binding sites from short reads generated by paired-end solexa ChIP-Seq technology. In this paper we used ChIP-Seq data from the Arabidopsis basic helix-loop-helix transcription factor ABORTED MICROSPORES (AMS), which is expressed within the anther during pollen development, the results show that SIPeS has better resolution for binding site identification compared to two existing ChIP-Seq peak detection algorithms, Cisgenome and MACS. Conclusions When compared to Cisgenome and MACS, SIPeS shows better resolution for binding site discovery. Moreover, SIPeS is designed to calculate the mappable genome length accurately with the fragment length based on the paired-end reads. Dynamic baselines are also employed to effectively discriminate closely adjacent binding sites, for effective binding sites discovery, which is of particular value when working with high-density genomes.




                And maybe some others.
                --------------
                Ethan

                Comment


                • #9
                  second that. at least it would be helpful to have one corresponding PE run to see how uneven fragment size distribution along the genome is. in addition the fragment size knowledge might provide important information on local chromatin structure. have a look at: www.ncbi.nlm.nih.gov/pubmed?term=21131275

                  Originally posted by yxibcm View Post
                  Actually, I would suggest using PE for ChIP-seq too. For SE reads, existing ChIP-seq software, such as MACS, shift and extend the reads to build the whole genome profile. The shift and extend distance was a fixed value estimated from the double peak pattern or provided by command line parameters. This might be inaccurate if the wrong shift/extend distance were used, and might cause the peak appear as doublets. So the peak heights are sensitive to the shift/extend values. PE sequencing provides fragment size information, therefore build whole genome profile is straightforward, no shift or extend involved. PE is also not that expensive compared with SE.

                  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
                  8 views
                  0 likes
                  Last Post seqadmin  
                  Started by seqadmin, Yesterday, 06:07 PM
                  0 responses
                  8 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
                  67 views
                  0 likes
                  Last Post seqadmin  
                  Working...
                  X