I received a lot of good help last time, and I hope someone will be able to help me this time as well. I've been working on an ngs pipeline exercise, and I've managed to make good progress, but I still have many questions regarding adaptor sequences and trimming. Keep in mind, I'm only a beginner at this.
1) Given a certain sequencing platform, how does one determine which adaptors were used to generate the reads? Is this information provided by the service provider? And if not provided, how does one determine which adaptors to search for?
2) If an adaptor is fragmented, how do you search/trim a certain percentage of it?
3) Do the adaptors differ between targeted sequencing, whole exome sequencing and whole genome sequencing
4) Is there software/tool that can automatically ID adaptors and fragments of adaptors within sequencing reads?
Thank you in advance!