Make Bowtie index for "ShortFuse" software.

[Palgrave]

I am about to try "ShortFuse" and they tell med to make a bowtie-index "... out of the genome and transcripts" I don't know what they mean:

Then, build the Bowtie index files

$ bowtie-build RefSeqTranscripts_50up_polyA.fasta refseq_transcripts

Then, you need to get reference file for the genome_plus_transcriptome
filtering step. You can obtain hg19 from

http://hgdownload.cse.ucsc.edu/goldenPath/hg19/bigZips/chromFa.tar.gz

You can obtain the transcriptome from

https://bitbucket.org/mckinsel/shortfuse/downloads/UCSC_genes.fa.gz

Then use bowtie-build again to make a Bowtie index out of the genome and
transcripts called transcripts_plus_genome in the ShortFuse_ref directory.