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Is it okay to use dna.toplevel file for alignment if primary assembly file is not available?

I cannot fine the primary assembly file for glycine max on ensembl plants. Can I use dna.top.level file or should i just stick to the sm files? I have read somewhere that "If the primary assembly file is not present, that indicates that there are no haplotype/patch regions, and the 'toplevel' file is equivalent.".

rnaseq index aligment ensembl hisat2
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updated by GenoMax GenoMax • written by pubsurfted • pubsurfted

1 answer

Yes you can use the top level file as indicated in help readme file.

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written by GenoMax GenoMax

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