2.9 years ago by
Well, Devon Ryan is right about RSEM.
However, I was just reading their tutorial, it seems like there is a way to extract transcripts sequences from genome. Of course you will have to have a genome fasta file and a gtf/gff file to run RSEM as below:
software/RSEM-1.2.25/rsem-prepare-reference --gtf ref/Mus_musculus.GRCm38.82.chr.gtf \
--bowtie2 --bowtie2-path software/bowtie2-2.2.6 \
The full tutorial is here: https://github.com/bli25ucb/RSEM_tutorial