Aligning RNA-Seq short reads to a reference gene with semi global alignment
Given a set of short reads from an RNA-Seq experiment and the reference sequence of a gene, my goal is to write an aligner to find out how much gene is expressed and locate the locations of its exons. Semi global alignment must be used, no end gap penalties. Could you advice me which tools could bu used or there is an aligner to use? If not I'll have to write the code by myself.
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Is this a homework assignment? If yes, you'll learned most by writing the code yourself in my opinion.
It is an assignment but instructor said that if there any ready aligners for that we can use them. We are not obligated to write a code.