SOLiD DeNovo assembly - Do I need to trim adaptors?

[DJParker]

Hello

This is perhaps a very naive question but I am use to working with basespace data....

We have done RNA-seq with SOLiD 5500XL paired-end reads and I was if I need to trim adaptors prior to assembly (with velvet, etc)?

And if so what would you use?

Thanks

Darren

[golharam]

No. The on-machine software removes the barcodes for you. If you have paired-end data, you should have 3 sets of files. 1 representing the forward reads, 1 representing the reverse reads, and 1 representing the barcodes. With the 5500, you probably have XSQ files instead of csfasta/qual files too. Good luck.