Question: changing header name in fasta file
0
gravatar for pong.singchat
2.2 years ago by
Bangkok, Thailand
pong.singchat0 wrote:

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 • 984 views
ADD COMMENTlink modified 2.2 years ago by Hugo280 • written 2.2 years ago by pong.singchat0
4

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.

ADD REPLYlink written 2.2 years ago by h.mon29k
2

'sed' would be great. I recommend it.

ADD REPLYlink written 2.2 years ago by Pierre Lindenbaum128k

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

ADD REPLYlink written 2.2 years ago by pong.singchat0
2

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

ADD REPLYlink written 2.2 years ago by st.ph.n2.5k
2

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,

ADD REPLYlink modified 2.2 years ago • written 2.2 years ago by natasha.sernova3.7k

Ohh

Its good for me

Big thanks

ADD REPLYlink written 2.2 years ago by pong.singchat0

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

ADD REPLYlink written 2.2 years ago by grant.hovhannisyan1.9k
0
gravatar for Hugo
2.2 years ago by
Hugo280
Universidade de Vigo, Ourense (Spain)
Hugo280 wrote:

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.

ADD COMMENTlink modified 12 months ago by RamRS27k • written 2.2 years ago by Hugo280

Thank you so much, Hugo Worapong

ADD REPLYlink written 2.2 years ago by pong.singchat0
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