Hi everyone! I'm a novice in bioinformatics and recently I've read a paper about RNA-mapping. In the article it says:

We mapped each of the paired-end reads separately using the commands “bwa aln fastqfile” and “bwa samse -n4”. In contrast to previous approaches, we mapped RNA-seq reads not only to the reference genome8,9 or to the transcriptome6,7 but to a combination of the hg19 reference genome plus exonic sequences surrounding all currently known splicing junctions from gene models available in annotation from Gencode, RefSeq, Ensembl and UCSC Genes.

I know that mapping RNA-seq reads by bwa aln and bwa samse, however, I cannot figure out how to map the reads to 'the hg19 reference genome plus exotic sequences surrounding all currently known splicing junctions'. Does it mean the blat correlation?

Thank you for your help!

Copen