Hi Guys, I intend on acquiring transcripts (cDNA) from certain human-cell line culture. I'd be acquiring all the reads using the MinION. The reads are expected to be 2-10kb (don't know yet the distribution).
From all the reads I obtain, I'd like to move forward to analysis with only certain read:
- The reads which will have a certain known tagging sequence (45 bases on the 3' end).
- The reads which will have and expected, known, open read frame (~2.5kb).
Obviously, I'd have to optimize the balance between sensitivity and specificity when targeting these reads.
Is there a tool designed for these specific types of screening? If not, would you suggest to write a code from scratch or revise an already somewhat-similar code?
I'm a novice to UNIX but have knowledge in coding (MATLAB, C), so keep that in mind please when answering.