I'm currently planning my first large RNA-seq experiment and was unsure about large-scale multiplexing.
I will have a total of 48 libraries and one option would be run 12 lanes with four libraries each. However, if it is possible, a better alternative would be to run all 48 libraries in each lane because 1) We could run an initial test lane to check quality and coverage and 2) we can easily scale up to run extra lanes to add required coverage.
With the Tru-seq RNA kit, they provide only 6 adapters per kit (12 with A and B kits combined) so I was wondering if anybody had any experience in making their own adapters, either using the older "in line" adapters or the newer method used by the Truseq kit with the separate seq read to determine the barcode. If so, are the results comparable to those using the commercial adapters and can they be easily substituted into the Truseq kit?
Any other alternative strategies or advice on the best way forward here would be greatly appreciated.
Thanks!
Stephen
I will have a total of 48 libraries and one option would be run 12 lanes with four libraries each. However, if it is possible, a better alternative would be to run all 48 libraries in each lane because 1) We could run an initial test lane to check quality and coverage and 2) we can easily scale up to run extra lanes to add required coverage.
With the Tru-seq RNA kit, they provide only 6 adapters per kit (12 with A and B kits combined) so I was wondering if anybody had any experience in making their own adapters, either using the older "in line" adapters or the newer method used by the Truseq kit with the separate seq read to determine the barcode. If so, are the results comparable to those using the commercial adapters and can they be easily substituted into the Truseq kit?
Any other alternative strategies or advice on the best way forward here would be greatly appreciated.
Thanks!
Stephen
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