changing header name in fasta file
1
0
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3.6 years ago

could you please help me to do this;

now I have head name like this:

>1
AAATAAAGTAACT
>2
ATCCCCTCCCTTA

and I need to edit it to

>contig_1 species name 
AAATAAAGTAACV
>contig_2 species name 
ATCCCCTCCCCC

Note; Can you recommend cat, grep, sed command, its will be great great for me.

Thank you so much..

sequence genome • 1.3k views
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4
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This is part of a long-running series called "google your own title".

There are so many good links I can't even choose one.

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'sed' would be great. I recommend it.

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Thank you so much could you please give me the command line?

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Try something. If you get stuck, or get an error - post the output and error message.

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See this post, for example:

A: Create list of sequences present in multiple FASTA files

See the right panel, there are usually a lot of similar question-answers there.

OR press "LATEST" button at the left upper corner, type some key-words there - it may halp. In you case:

rename fasta file or something similar,

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Ohh

Its good for me

Big thanks

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If you know a bit of python you can give a try to Biopython SeqIO module.

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3.6 years ago
Hugo ▴ 340

Dear colleague,

I will recommend you to try SEDA. The "Rename header" option (explained in section 3.8 of the user manual) allows you to do exactly what you need.

With best regards,

Hugo.

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Thank you so much, Hugo Worapong

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