Generating reference from exome sequence data(bam) to map RNA seq(fastq) from the same individual

Question

[seqlearner]

Is it possible to generate a reference from exome sequenced/aligned(BWA MEM 0.7.10) to map the RNAseq data from the same individual?The idea is to reduce the mapping bias in RNA seq mapping to the common hg19 reference.

I would appreciate some advice/suggestions on tools at different steps.

Thanks in advance

[Ashutosh Pandey]

Yes, it is possible. This question has already been discussed several times on this forum. Please use the search feature to find them. At the same time I will keep the question open to get some fresh insights into this topic here.

Answer 1

[Brian Bushnell]

If you want to reduce ref bias, I recommend you use a very sensitive aligner such as BBMap rather than mutating the reference in order to align with a less-sensitive aligner. Using a different reference for every experiment can cause major headaches later on when coordinates and base calls no longer match the annotation.