I am looking to align some 40 dna sequences against an RNA-seq run that I've prepared using tophat and bowtie and I believe there must be a very simple way to see if these sequences show up in a resulting new splice variant.
I have all the right tools in place at this point, created a bowtie index file of my reference sequence, ran the analysis through the bulk of the tuxedo suite -- without error -- it is color solid run and I ran it against hg19_c.
So that's good. Now I am sitting at the end and wanting to just do basically a blast it seems or a new alignment which should tell me whether these sequences I have align with the resulting data.
Am I incorrect in assuming this should be straightforward to do?
I have all the right tools in place at this point, created a bowtie index file of my reference sequence, ran the analysis through the bulk of the tuxedo suite -- without error -- it is color solid run and I ran it against hg19_c.
So that's good. Now I am sitting at the end and wanting to just do basically a blast it seems or a new alignment which should tell me whether these sequences I have align with the resulting data.
Am I incorrect in assuming this should be straightforward to do?