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Old 01-03-2016, 02:39 AM   #1
JosefienVanLanduyt
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Post Convert .fna file from NCBI to .fa or .fasta file

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
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Old 01-03-2016, 04:31 AM   #2
mastal
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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.
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Old 01-03-2016, 05:10 AM   #3
JosefienVanLanduyt
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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?
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Old 01-03-2016, 05:16 AM   #4
GenoMax
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Just rename the .fna extension to .fa (as long as the file is in fasta format). That should work.

Code:
$ cp file.fna file.fa
If you are not sure about the format of the file post the output of this command
Code:
$ head -10 file.fna
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Old 01-04-2016, 04:52 AM   #5
JosefienVanLanduyt
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Quote:
Originally Posted by GenoMax View Post
Just rename the .fna extension to .fa (as long as the file is in fasta format). That should work.

Code:
$ cp file.fna file.fa
If you are not sure about the format of the file post the output of this command
Code:
$ head -10 file.fna
thank you very much it is working now !
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Old 01-17-2019, 07:19 AM   #6
hira
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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?
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Old 01-17-2019, 08:21 AM   #7
GenoMax
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No the results will not be affected since we are not changing sequence/content of any data files. We are only renaming the file.
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Old 01-17-2019, 09:08 AM   #8
hira
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will the content is same in both files?
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Old 01-17-2019, 10:00 AM   #9
GenoMax
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Yes. As long as you only change the file name.
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Old 01-17-2019, 10:06 AM   #10
hira
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Thank you for your help
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