length reads after trimming

[pingu]

Hello!
I have to trim primers of my reads, after trimming are there a length of reads suggest? So I would understand if I have to discard short reads. My analysis is on DNA.
Thank you very much in advance

[Brian Bushnell]

You should discard reads too short to use for what you are doing. That said - you have not said what you are doing, or what length of reads you are starting with, so it's impossible to say. What is your read length, insert size distribution, and experiment?

[pingu]

Thank you very much for your response. I am implementing my pipeline in order to analyse BRCA1 and BRCA2. The initial length of the reads is about 300bp, I don't know distribution of insert size, how I can find it?
thank you in advance

[GenoMax]

You can do insert size estimate by BBMap/BBMerge like this: http://seqanswers.com/forums/showpos...13&postcount=2

That said for good libraries you should hardly have any adapter contamination. Why are you worried about short reads in a 300 bp run?