Replacing FASTA headers for TopHat & Cufflinks

brachysclereid

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Join Date: Feb 2011

Posts: 32
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#1

Replacing FASTA headers for TopHat & Cufflinks

02-15-2011, 01:15 PM

Hi,

Does anyone know how to replace all the headers in a FASTA file with new names given in another list? The FASTA headers in the genome file are very complex. In the gtf file it just says scaffold1, scaffold2, etc. I need to replace each complex name with the corresponding simple name.

Any tools out there?
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maubp

Peter (Biopython etc)

Join Date: Jul 2009

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02-16-2011, 02:32 AM

It sounds like a straight forward scripting task - can you program in Perl, Python, Ruby, ...?
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brachysclereid

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#3

02-16-2011, 05:44 AM

programming

Thanks,
I was able to solve this problem. I am starting to program. For common tasks like this I just assumed there would be some little program already out there.
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