Change accession number to chromosome number in reference genome
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17 months ago
Tsigabu • 0

I have a reference genome explained by accession number instead of chromosome number. Any clue how to convert it into a chromosome number in the Linux terminal? Any suggestion is kindly appreciated.

fasta chromosome • 976 views
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Could you provide an example for your question, including the input and desired output? This will make it easier to assist you.

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Thanks for the reply. As displayed below, the fasta reference file is starting with >NC_, but what I'm looking for is I need to substitute the accession number by Chromosome number. For-example, the accession number NC_056070.1 stands for chromosome 17. instead of starting the first column with NC_056070.1 I need Chromosome 17. The fast file has 26 chromosomes, X chromosome and mitochondrial sequence as well.

kindly.

>NC_056070.1 Ovis aries strain OAR_USU_Benz2616 breed Rambouillet chromosome 17, ARS-UI_Ramb_v2.0, whole genome shotgun sequence
>NC_056071.1 Ovis aries strain OAR_USU_Benz2616 breed Rambouillet chromosome 18, ARS-UI_Ramb_v2.0, whole genome shotgun sequence
>NC_056072.1 Ovis aries strain OAR_USU_Benz2616 breed Rambouillet chromosome 19, ARS-UI_Ramb_v2.0, whole genome shotgun sequence
>NC_056073.1 Ovis aries strain OAR_USU_Benz2616 breed Rambouillet chromosome 20, ARS-UI_Ramb_v2.0, whole genome shotgun sequence
>NC_056074.1 Ovis aries strain OAR_USU_Benz2616 breed Rambouillet chromosome 21, ARS-UI_Ramb_v2.0, whole genome shotgun sequence
>NC_056075.1 Ovis aries strain OAR_USU_Benz2616 breed Rambouillet chromosome 22, ARS-UI_Ramb_v2.0, whole genome shotgun sequence
>NC_056076.1 Ovis aries strain OAR_USU_Benz2616 breed Rambouillet chromosome 23, ARS-UI_Ramb_v2.0, whole genome shotgun sequence
>NC_056077.1 Ovis aries strain OAR_USU_Benz2616 breed Rambouillet chromosome 24, ARS-UI_Ramb_v2.0, whole genome shotgun sequence
>NC_056078.1 Ovis aries strain OAR_USU_Benz2616 breed Rambouillet chromosome 25, ARS-UI_Ramb_v2.0, whole genome shotgun sequence
>NC_056079.1 Ovis aries strain OAR_USU_Benz2616 breed Rambouillet chromosome 26, ARS-UI_Ramb_v2.0, whole genome shotgun sequence
>NC_056080.1 Ovis aries strain OAR_USU_Benz2616 breed Rambouillet chromosome X, ARS-UI_Ramb_v2.0, whole genome shotgun sequence
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If the above is a consistent pattern, edit the header so it has just the chromosome [^,]+ but as chromosome_[^,]+ like so:

sed -Ee '^>s/.+chromosome ([^,]+),.+/chromosome_\1/' in.fasta > renamed.fasta

Test before running on the whole file and double check headers once done.

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