I am studying the recombination event in positive-stranded RNA viruses. I have performed HiSeq 2000 illumina paired-end sequencing on a specific region of viral RNA. I have received the results, and aligned all the reads to the reference sequence using bowtie ( I have not used tophat, as I am dealing with one splice junction point, plus I have got a recombinant sequence as ref. to align against ). I succeeded to view my reads on IGV. Now, I want to assemble my reads to get the viral RNA sequences to study the sequence-specific recombinants. I want to retrieve all sequences which are represented by reads. I am really confused how to do that!
Appreciate your help.
Appreciate your help.