Refernece Genome for Wheat (Rna-seq) with Hisat2

hira · 01-17-2019, 07:29 AM

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.

GenoMax · 01-17-2019, 08:22 AM

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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01-17-2019, 07:29 AM	#1
hira Junior Member Location: Federal Pakistan Join Date: Jan 2019 Posts: 4	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.

01-17-2019, 08:22 AM	#2
GenoMax Senior Member Location: East Coast USA Join Date: Feb 2008 Posts: 6,845	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?