Thread: bwa alignement
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Old 08-24-2020, 11:54 AM   #2
GenoMax
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Location: East Coast USA

Join Date: Feb 2008
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What is not working properly? Indexing genome and alignment are two independent steps. You completed the indexing of the genome. Now you need to align using `bwa mem`+ this index + your reads => Aligned SAM file => Aligned BAM file.

You could give your database a name that is what the "prefix" refers to. If you don't provide a name then your index is going to use the same "basename" as your reference file. In this case, "reference.fasta".
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