Let me start of by saying, I have very very limited knowledge with regards to NGS and I'm truly the definition of a beginner. I have a couple of questions regarding certain steps during pre-processing of sequencing data from ANY platform, sorry if this has been asked before.
1) Given a fastq file (from any platform), how does one identify the location and orientation of an adaptor sequence?
2) How does one define the minimum bp length to infer adaptor? Or otherwise, if I'm working with a given fastq file, and I grep the adaptor sequence, obviously the full adaptor sequence doesn't appear in all the reads, so how low can I go with the amount of bp in the adaptor sequence I grep for?
Hopefully these questions make sense.