align reads to a custom reference genome

Question

[Amina]

Hello,

I want to insert a specific sequence into the reference genome mm10 and then use it for alignment. Does anyone know how to do that?

Answer 1

[ATpoint]

Make a fasta file with that sequence. Use cat genome.fa newSequence.fa > extendedGenome.fa to append it to the reference genome. Index that new file with the aligner and slign as usual.

[colindaven]

It's a good idea to generate fasta index by running samtools faidx extendedGenome.fa and check things are as expected too.