Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Resequencing

    Hey all,
    i had a full run in Miseq (250 samples). I work with qiime, after the sequencing i saw i needed to resequence several samples so i entered the run with a colleague who also resequenced some of his samples. Now the problam is that i dont know if the denovo's i get from the second run are the same as the first. so i want to extract only my samples from the second run and then re-do the qiime pipline to make sur each unique read actually gets it own denovo no.
    Any suggestions/alternatives?
    Thanks

  • #2
    Did your samples have unique barcodes? If they did then you should be able to use only your data. If they did not then there is not much you are going to be able to do with this run (if fact your colleague can't use this data either).

    Comment


    • #3
      GenoMax

      Each sample had a unique bacode in our first run. but when we repeated each sample remained with its former barcode (we only have 250 barcodes)

      Comment


      • #4
        Did your samples have unique barcodes (that were independent from your colleague's) when you did the second run? If some of the sample barcodes overlapped then those samples would be non-usable in second run.

        Comment


        • #5
          Yes. our sample are not overlapping in barcodes

          Comment


          • #6
            Great. If the samples from run 1 and 2 are the same set then you can re-run your Qiime pipeline using the pooled set of sequences leading to a single result.

            Comment


            • #7
              1. i have the same barcodes from the second run in my first (only 7 samples)
              2. Im sorry but i didnt understand what you wrote (im still new in this)

              Comment


              • #8
                Let me see if my understanding is correct.

                You have 7 samples that you ran on Run 1. You decided that the number of reads was not enough so you ran the same set of samples a second time. Since the same set of libraries ran a second time (think of it as a technical sequencing replicate) you can merge the sample data sets from the 2 runs into single file for each sample and re-run your Qiime pipeline.

                Does this not address your original question?

                Comment


                • #9
                  You undertood correct.
                  And i understand what you mean, but how can i do that without merging my colleague's samples? (in my first run i have barcodes with the same number?
                  And, how can i know that for example the qiime give a read the number denovo5 in my 1st run but will give the same sequence denovo70 in the second?

                  Comment


                  • #10
                    Are you working with demultiplexed files or otherwise? If the data is demultiplexed then your samples should have been separated from your colleagues, correct?

                    Comment


                    • #11
                      How can i know if my data is a demultiplexed files?
                      I have the Miseq out files (R1,R2,I1) from each sequence run

                      Comment


                      • #12
                        Sounds like the runs are not demultiplexed, if you only have 3 files for each run.

                        It may be best to demultiplex the two runs so you can separate out your colleague's data from run 2 and then merge the fastq files for each of your samples from the two runs. Demultiplexing can be done using this script: http://qiime.org/scripts/split_libraries_fastq.html

                        Comment


                        • #13
                          OK. Thank yo very much!

                          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
                          11 views
                          0 likes
                          Last Post seqadmin  
                          Started by seqadmin, Yesterday, 06:07 PM
                          0 responses
                          10 views
                          0 likes
                          Last Post seqadmin  
                          Started by seqadmin, 03-22-2024, 10:03 AM
                          0 responses
                          51 views
                          0 likes
                          Last Post seqadmin  
                          Started by seqadmin, 03-21-2024, 07:32 AM
                          0 responses
                          68 views
                          0 likes
                          Last Post seqadmin  
                          Working...
                          X