Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Any tricks? 244 sample SampleSheet.csv using NextSeq?

    We are sequencing a pool of 244 samples on our new (now obsolete?) NextSeq500. First time with over 96 samples. Can we just make one SampleSheet.csv with the 244 samples and their indecies (indexes?), and, will the bcl2fastq.pl script work? *Note* The bcl2fastq.pl script is being "managed" by the HPC center, so I didn't install it, and honestly don't know much about it yet.

    Thanks!

    -p

  • #2
    Yes. Use Illumina experiment manager (windows only, download from Illumina) to make the samplesheet (if you don't have a prior example). I have done 9000+ samples in a single sheet without any problems as long as your indexes have no collisions/sample names are in right format (no space, odd characters etc).

    Comment


    • #3
      Originally posted by GenoMax View Post
      Yes. Use Illumina experiment manager (windows only, download from Illumina) to make the samplesheet (if you don't have a prior example). I have done 9000+ samples in a single sheet without any problems as long as your indexes have no collisions/sample names are in right format (no space, odd characters etc).
      Great, thanks. We have IEM and should be able to handle the index names.

      Comment


      • #4
        Remember to run dos2unix on SampleSheet.csv if you move the samplesheet directly from your PC to the server otherwise you should be all set.

        Comment


        • #5
          Hmmm,
          Actually, the IEM only gives me the option of 96-well plates. Do we need to manually create a new 384-well plate file first? Or use a HiSeq option?

          Comment


          • #6
            Use create SampleSheet option on main screen and then NextSeq. It may be painful to do 244 rows this way though. You could just get a sample and then edit outside IEM.

            Comment


            • #7
              Originally posted by GenoMax View Post
              Use create SampleSheet option on main screen and then NextSeq. It may be painful to do 244 rows this way though. You could just get a sample and then edit outside IEM.
              Tried both ways. Nope. I can't figure it out. IEM accepts the SamplePrepKit file with 384 wells. But when I try to load a plate with 384 wells I get an error saying "Index was outside the bounds of the array". I've made custom plates and assays before.

              Anyone with a NextSeq have a 384-well SampleSheet, or plate file, that works?

              Calling Illumina now...

              *EDIT* I was able to add rows to the SampleSheet manually from within IEM. I could never get a plate to load or edit with 384 wells. It was a PITA but now I have a Sample template to work with. Still don't know if it'll work but according to GenoMax, it should. Thanks.
              Last edited by hoytpr; 07-20-2017, 12:57 PM. Reason: Want to be clear and correct.

              Comment


              • #8
                Your samplesheet does not need to be generated by IEM.
                IEM is a nice tool, so you get the headers, parameters etc right.

                But you can also easily open the resulting .csv in excel and add how many rows you wish.
                Last edited by Genetic Librarian; 07-26-2017, 04:43 AM.

                Comment


                • #9
                  Just wanted to thank y'all for your help. All 200+ samples processed perfectly on the first try.

                  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
                  34 views
                  0 likes
                  Last Post seqadmin  
                  Started by seqadmin, 03-08-2024, 08:03 AM
                  0 responses
                  72 views
                  0 likes
                  Last Post seqadmin  
                  Started by seqadmin, 03-07-2024, 08:13 AM
                  0 responses
                  81 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