Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • #16
    Multiplex (12-plex) Illumina Adapter/Primer Sequences

    Hi,

    Has anyone got the multiplex oligo sequences that Illumina use in their Multiplex (12-plex) kits? (And their concentrations if they're known.)

    Comment


    • #17
      Originally posted by bioinfosm View Post
      Hi all,

      Thanks for the technical details on this. Anyone got some information about bioinformatics on adapter contamination detection and removal. I tried using adapter sequences with eland to check for contamination, but less than 1% reads aligned. I expected more as less than 10% reads aligned to actual reference.

      I know of a file one can specify in GA pipeline, to exclude sequences -- could someone point more details on the same? (i tried bioinformatics thread, but did not hear back )

      thanks!
      novoalign has 5' and 3' removal of adapter sequences prior to alignment. works well.
      david

      Comment


      • #18
        Hi,

        I run the site you got the sequences from and am happy to see that you have posted the info here as well. I will attempt to keep the list up to date as new sequences are released. If there is any additional info you would like, let me know and I'll post it if possible.

        Cheers,

        Brent

        Comment


        • #19
          Hey Brent,

          Nice to have you, thanks for being willing to share with the community. I'm sure everyone would appreciate any info you have.

          Comment


          • #20
            Adapter sequence

            i know that the overhanging T is used to ligate with the added A from the DNA library, but thy is there a one base pair overhang on the other side? If you see how the sequence anneal there is an overhang on both ends. Both adapter sequences are 33 bases. If you only wanted the T overhang, why wouldn't you have 32 bases on one strand and 33 on the strand with the T overhang?

            Comment


            • #21
              which adapters to use

              Hi all,
              I have a question:
              I've prepared a cDNA library for solexa (double stranded) with 5' end after enzymatic cleavage by MMEI (see below). I would like to perform a single read from 5' (the left side with the MME sticky end). GEX2 adapter fits this site. My question is which adapter do I need for the 3' side to perform a single read of the 5' side (left side)?

              5'_________? 3'
              adapter Gex 2 3'___________
              (MMEI side) which adapter on this side?

              Can anyone answer this???

              Comment


              • #22
                the figure came out wrong... I hope you can still understand my question above....

                Comment


                • #23
                  Do pages 17 - 20 of this help?

                  Comment


                  • #24
                    yes it helps, thank you

                    Comment


                    • #25
                      Perhaps the sequences are shown in Figure 2 and table S3 of this paper by Craig et al (http://www.nature.com/nmeth/journal/...th.1251.html)? I notice one of the authors has an Illumina affiliation and the paper describes 6 bp error corrected tags. Of course, they don't tell you outright which ones are the best but my guess is the 13 tags showing less than 2-fold difference in index frequencies between runs (Fig 2).

                      Originally posted by breakt1000 View Post
                      Hi,

                      Has anyone got the multiplex oligo sequences that Illumina use in their Multiplex (12-plex) kits? (And their concentrations if they're known.)

                      Comment


                      • #26
                        comparison of SE and PE sequences

                        Hi all
                        I put together a comparison of SR and PE sequences to get a quick look at regions of sequence similarity. Thought it might be useful for others (let me know if you spot errors). As far as I can tell, the SR and PE read 1 sequencing primers are identical, as are the SR and PE adapters with the T overhang. Seems to me that given this, it should be fine to run a PE library on an SR flowcell using SR reagents. Comments?
                        All the sequences are from the Bentley et al. nature paper supplementary info last year.
                        Attached Files

                        Comment


                        • #27
                          thank

                          yes it help,thank

                          Comment


                          • #28
                            thank,
                            Has anyone got the multiplex oligo sequences that Illumina use in their Multiplex (12-plex) kits? (And their concentrations if they're known.)

                            Comment


                            • #29
                              Hi!
                              I am trying to add adapters onto a cDNA pool by PCR. Has anyone done this before? I not sure how to design and orient my primers. I am currently looking to use the adapters for "Genomic DNA oligonucleotide sequences"
                              Thanks!
                              Kate

                              Comment


                              • #30
                                Does anyone happen to know the concentrations of the PR 5' adapter and the 10x v1.5 sRNA 3' adapter in the small RNA cloning kits?

                                Comment

                                Latest Articles

                                Collapse

                                • 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
                                • seqadmin
                                  The Impact of AI in Genomic Medicine
                                  by seqadmin



                                  Artificial intelligence (AI) has evolved from a futuristic vision to a mainstream technology, highlighted by the introduction of tools like OpenAI's ChatGPT and Google's Gemini. In recent years, AI has become increasingly integrated into the field of genomics. This integration has enabled new scientific discoveries while simultaneously raising important ethical questions1. Interviews with two researchers at the center of this intersection provide insightful perspectives into...
                                  02-26-2024, 02:07 PM

                                ad_right_rmr

                                Collapse

                                News

                                Collapse

                                Topics Statistics Last Post
                                Started by seqadmin, 03-14-2024, 06:13 AM
                                0 responses
                                32 views
                                0 likes
                                Last Post seqadmin  
                                Started by seqadmin, 03-08-2024, 08:03 AM
                                0 responses
                                71 views
                                0 likes
                                Last Post seqadmin  
                                Started by seqadmin, 03-07-2024, 08:13 AM
                                0 responses
                                79 views
                                0 likes
                                Last Post seqadmin  
                                Started by seqadmin, 03-06-2024, 09:51 AM
                                0 responses
                                68 views
                                0 likes
                                Last Post seqadmin  
                                Working...
                                X