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What does header of Reference database fasta file has to look like ? #49

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arpit20328 opened this issue Sep 10, 2024 · 2 comments
Open

What does header of Reference database fasta file has to look like ? #49

arpit20328 opened this issue Sep 10, 2024 · 2 comments

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@arpit20328
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arpit20328 commented Sep 10, 2024 •
edited by shenwei356
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So my Reference fasta header is like

>kraken:taxid|520|NZ_CP018042.1 Bordetella pertussis strain J313 chromosome, complete genome
ATGGATTTTCCCCGCGAATTTGATGTGATCGTCGTTGGTGGCGGTCACGCCGGTACGGAG
GCAGCCCTGGCTGCAGCCCGCGCCGGCGCACAGACATTGCTGCTTACCCACAATATCGAG
ACCCTGGGCCAAATGTCCTGCAATCCCTCCATCGGGGGGATAGGCAAGGGTCATTTGGTC
AAGGAAGTCGATGCGTTGGGCGGCGCGATGGCTATCGCCACCGACGAGGCAGGTATCCAA
TTCCGTATTCTCAACAGCTCCAAGGGGCCAGCGGTACGTGCCACGCGTGCCCAAGCCGAC
CGGGTGCTGTACCGAAACGCCATACGTGCACAGCTCGAGAACCAGCCCAACCTCTGGCTG
TTCCAGCAGGCGGTGGACGATCTGATGGTGCAGGGCGACCAGGTGGTGGGCGCCGTTACG
CAGATCGGGTTGCGCTTTCGTGCCCGTACCGTGGTGCTGACGGCTGGGACCTTCCTCAAC
GGTTTGATTCACGTGGGGCTGCAGAACTATTCCGGAGGGCGGGCAGGGGATCCTCCCGCC

Should I make it like the following:

>NZ_CP018042.1
ATGGATTTTCCCCGCGAATTTGATGTGATCGTCGTTGGTGGCGGTCACGCCGGTACGGAG
GCAGCCCTGGCTGCAGCCCGCGCCGGCGCACAGACATTGCTGCTTACCCACAATATCGAG
ACCCTGGGCCAAATGTCCTGCAATCCCTCCATCGGGGGGATAGGCAAGGGTCATTTGGTC
AAGGAAGTCGATGCGTTGGGCGGCGCGATGGCTATCGCCACCGACGAGGCAGGTATCCAA
TTCCGTATTCTCAACAGCTCCAAGGGGCCAGCGGTACGTGCCACGCGTGCCCAAGCCGAC
CGGGTGCTGTACCGAAACGCCATACGTGCACAGCTCGAGAACCAGCCCAACCTCTGGCTG
TTCCAGCAGGCGGTGGACGATCTGATGGTGCAGGGCGACCAGGTGGTGGGCGCCGTTACG
CAGATCGGGTTGCGCTTTCGTGCCCGTACCGTGGTGCTGACGGCTGGGACCTTCCTCAAC
GGTTTGATTCACGTGGGGCTGCAGAACTATTCCGGAGGGCGGGCAGGGGATCCTCCCGCC

@shenwei356 Please help.
@shenwei356
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I depends on you.

@shenwei356
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Sorry, I should comment more. I mean, the sequence header is not important, cause they are not used.

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@shenwei356 @arpit20328