Align unmapped reads to reference vector sequence

Question

[Tonkatsu]

Hi, I was wondering if anyone had any suggestions for aligning the unmapped reads (from my rna-seq data) to a short reference sequence?

I already have the unmapped reads in fastq and the short reference sequence in fasta format.

Answer 1

[swbarnes2]

The smartest way to do this is to make a new reference which includes your vector sequence and redo the whole alignment or pseudo-alignment.

Or, just use, say, bwa, to index and align.