I’ve downloaded my genome reference index from NCBI ( Human Build 38 patch release 13 (GRCh38.p13).
The downloaded assembly is in fasta.tar format. I ran bowtie2 for mapping and used the command:
bowtie2-build genome_assemblies_genome_fasta.tar bowtie the output is: Warning: Encountered empty reference sequence Warning: Encountered reference sequence with only gaps Reference file does not seem to be a FASTA file
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