Convert .fna file from NCBI to .fa or .fasta file

[hira]

Thank you for your help

[GenoMax]

Yes. As long as you only change the file name.

[hira]

will the content is same in both files?

[GenoMax]

No the results will not be affected since we are not changing sequence/content of any data files. We are only renaming the file.

[hira]

could you please explain that changing the file extension won't effect the results for which we are mapping with a reference genome in case of RNA-seq for HISAT2 software?

[JosefienVanLanduyt]

Just rename the .fna extension to .fa (as long as the file is in fasta format). That should work.

$ cp file.fna file.fa

If you are not sure about the format of the file post the output of this command

$ head -10 file.fna

thank you very much it is working now !

[GenoMax]

Just rename the .fna extension to .fa (as long as the file is in fasta format). That should work.

$ cp file.fna file.fa

If you are not sure about the format of the file post the output of this command

$ head -10 file.fna

[JosefienVanLanduyt]

The problem is; STAR is not recognizing this fasta format (.fna), I am getting an error that is impossible to read this fasta file, that why I wondered if it was not possible to convert from .fna to .fa. Or do you think it is a problem with the file itself and STAR is able to read/load .fna files?

[mastal]

As far as I know, .fna just means fasta nucleic acid (as opposed to .faa, fasta amino acid, for protein sequences), so the file is actually in fasta format.

[JosefienVanLanduyt]

Hello,
I am totally new to this (I am a student following a course in bio-informatics) and I wanted to use a genome found on NCBI (in .fna or genbank format with .gff annotation) as a reference genome in STAR as an exercise but I cannot find a way to convert the .fna file so the genome can be read by STAR in --genomeFastaFiles. It is a genome not found on normal genome database sites (UCSC e.g.) since it is from a copepod and not much genomic work is done on copepods...
Is this even possible to use such a genome as a reference genome or is this a bad idea from the start?
Thank you in advance,
kind regards,
Josefien