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  • hira
    Junior Member
    • Jan 2019
    • 5
    #1

    Refernece Genome for Wheat (Rna-seq) with Hisat2

    How can i Download Reference genome of Wheat (triticum aestivum) as index for mapping (with RNA-seq) by HISAT2.
    The file i accessed from NCBI is with the extension of .fna and the software accepts .fa files.
    i am confused the if i changed the extension .fna to fa will it effect the results for rna-seq data.
    Tags: .fa file, fnafile, hisat2, referencegenome, rna-seq
    • GenoMax
      Senior Member
      • Feb 2008
      • 7142
      #2
      NCBI uses ".fna" (for nucleotide) and ".faa" (for protein) fasta format files. Changing the file extension to ".fa" will not affect results. HISAT2 should be able to use the ".fna" file as is. Is it complaining?

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