I aligned my reads to de novo transcriptome using bowtie. Now the unaligned reads from the previous step was mapped to genome using tophat2. Now I would like to count the reads mapped to every scaffold and along the coverage region. How can I achieve this as tools like tophat,feature counts requires gtf file which has location of transcripts in every scaffold.But here the unaligned reads are mapped outside of the transcripts and hence I dont know whether using GTF file will be appropriate.
Any guidance wil be highly useful.
Thanks in advance