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.nt assemblage file, can I convert to FASTA?

Hi all

I've been given a .nt (never come across these before) file of a bacterial genome which I want to index to use with bowtie but bowtie accepts .fasta and not .nt. Could you guys explain what the hell a .nt file is and can I convert it to .fasta?

Huge thanks in advance!

fasta file usage mapping bowtie
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written by YOUSEUFS • YOUSEUFS

Have you tried looking at the contents of the file? It is probably an incorrectly named fasta file.

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written by Brian Bushnell Brian Bushnell

The first few lines look like this (it might not show correctly here) 

....|....| ....|....| ....|....| ....|....| ....|....| ....|....|

 5          15         25         35         45         55    
scaffold00   ttggttaggt aaggaagtag tattgctact actccctccc ttagaaacgc agcatgcagg

scaffold00   ttctgctata tatctatttc cgtgagaatc cttgcagaga acatcaacaa tactttgttt

scaffold00   caacttaatt agaagtttag ctttaacttt aaatggacta ctcaaccgtg acagacttag
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updated by Pierre Lindenbaum Pierre Lindenbaum • written by YOUSEUFS • YOUSEUFS

That looks like Phylip, which is a really irritating format to deal with. I'd just ask the person for a fasta file instead, or download one yourself if you know the exact bacterial strain.

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written by Brian Bushnell Brian Bushnell

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