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bowtie2

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
genome mapping
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updated by Friederike Friederike • written by gina02 • gina02

1 answer

You will probably have to un-tar the genome first (.tar indicates that you downloaded a compressed collection of files). The command to do that is tar -xvf <tar file name with .tar extension>, you can find more details e.g. here

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written by Friederike Friederike

I ran your command and im getting this: zsh: parse error near `\n'

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written by gina02 • gina02

When exactly does the error occur? Can you post the exact command that triggers it?

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written by Friederike Friederike

I made a mistake it works fine now thanks a lot

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written by gina02 • gina02

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