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Align unmapped reads to reference vector sequence

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.

rna-seq fasta alignment fastq
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updated by swbarnes2 swbarnes2 • written by Tonkatsu • Tonkatsu

1 answer

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.

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written by swbarnes2 swbarnes2

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