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