Hello,

Well this is my first question about bioinformatics. I am starting from scratch bioinformatic analysis so sometimes I found some problems that I am can´t solve. At this moment I am trying to make and RNA-editing analysis using the protocol that was used in this paper (Dynamic landscape and regulation of RNA editing in mammals, Nature, 2017). The problem that I found is in the first step, mapping the RNA-seq reads to the genome. In the supplemental information they write the following:

In brief, we used BWA to align RNA-seq reads to a combination of the reference genome and exonic sequences surrounding known splicing junctions from available gene models. We mapped each of the paired-end reads separately using the commands ‘bwa aln fastqfile’ and ‘bwa samse -n4’. We chose the length of the splicing junction regions to be slightly shorter than the RNA-seq reads to prevent redundant hits (that is, 95 bp for reads of 100 bp length)."

Now comes my question, how can i make the index to map the reads with those parameters (reference genome+exonic sequences surrounding known splicing junctions, and choosing the lenght of the splicing junctions shorter than the reads)? The problem is thatv I don´t know where i cant find the "exonic sequences surrounding splicing junctions" neither to make the BWA index choosing the lenght for that splicing junctions regions making then slightly shorter than the RNA-seq reads.

I hope that I had explained clearly my question and I would be grateful for any help that anyone can provide.

Thanks in advance.