Help, I'm having problem with bwa mapping

Question

[davidcopen]

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

Answer 1

[Charles Plessy]

You have to create a BWA index containing "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". If the authors did not leave a more detailed description of the contents, the only way to reproduce what they did will be to contact them and ask for more precise information.

Answer 2

[h.mon]

I don't have the faintest idea of what "the blat correlation" is.

This protocol seems overly convoluted, using a genome supplemented with exonic sequences surrounding splice junctions, probably to account for the fact BWA is not splice aware. You would be better off using STAR or HISAT2.