how many cycles to run for truseq small RNA libraries

wingtec · 05-05-2014, 09:16 AM

Hi All,

I wonder how many cycles others choose to run for TruSeq small libraries and if they will select the option of trimming the adaptor sequences.

Thanks

Wingtec

nucacidhunter · 05-06-2014, 06:12 PM

SBS kits with minimum 50 cycle is offered for HiSeq and MiSeq systems, so 50 cycle is normally used for sequencing small RNA libraries. From your post I assume you want to sequence them on MiSeq system. Adapter trimming is required as the small RNA is shorter than 50 base, but an offline software would do better job trimming than MiSeq onboard software. A 5% PhiX spiking also will help with sequencing quality as samll RNA libraries usually are low diversity.

wingtec · 05-07-2014, 08:05 AM

Thank you for your answer, NUACIDHUnTER! This is assuring.

Wingtec

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05-05-2014, 09:16 AM	#1
wingtec Member Location: Charlottesville, VA Join Date: Apr 2010 Posts: 34	how many cycles to run for truseq small RNA libraries Hi All, I wonder how many cycles others choose to run for TruSeq small libraries and if they will select the option of trimming the adaptor sequences. Thanks Wingtec

05-06-2014, 06:12 PM	#2
nucacidhunter Jafar Jabbari Location: Melbourne Join Date: Jan 2013 Posts: 1,238	SBS kits with minimum 50 cycle is offered for HiSeq and MiSeq systems, so 50 cycle is normally used for sequencing small RNA libraries. From your post I assume you want to sequence them on MiSeq system. Adapter trimming is required as the small RNA is shorter than 50 base, but an offline software would do better job trimming than MiSeq onboard software. A 5% PhiX spiking also will help with sequencing quality as samll RNA libraries usually are low diversity.

05-07-2014, 08:05 AM	#3
wingtec Member Location: Charlottesville, VA Join Date: Apr 2010 Posts: 34	Thank you for your answer, NUACIDHUnTER! This is assuring. Wingtec