how many cycles to run for truseq small RNA libraries

[wingtec]

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]

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]

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

Wingtec