Closed:Process RNA-Seq Data with specific sequences / not whole reference genome

Question

[Heinrich_M]

I have specific sequences that I should quantify in RNA-Seq data. First, I blast the sequences against the reference genome. Now these data have to be compared with the reads of the RNA-Seq analyses. I used the specific sequences in Bowtie 2 as reference genome (fa format) and mapped the RNA-Seq data with them. It worked, but is this the right way? I also have to count the mapped reads, but it doesn't work with htseq-count because the identifier is not unique. How can I solve this problem?