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Old 07-20-2017, 08:44 AM   #1
hoytpr
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Question 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
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Old 07-20-2017, 08:59 AM   #2
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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).
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Old 07-20-2017, 09:03 AM   #3
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Quote:
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.
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Old 07-20-2017, 09:06 AM   #4
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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.
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Old 07-20-2017, 09:09 AM   #5
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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?
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Old 07-20-2017, 09:11 AM   #6
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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.
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Old 07-20-2017, 12:00 PM   #7
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Quote:
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 at 12:57 PM. Reason: Want to be clear and correct.
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Old 07-20-2017, 11:53 PM   #8
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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 at 04:43 AM.
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Old 07-24-2017, 06:26 AM   #9
hoytpr
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Thumbs up

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