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Old 03-03-2014, 08:18 AM   #1
seema12345
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Default Reverse complement of a bacterial gene

Hello everyone,

I am trying to create reverse complement of a bacteria gene in minus strand. Though I have read a lot on its mechanism and even got a perl script done that generates reverse complement of a sequence in Fasta format.
But, I need to generate it for bases in rows, with separate columns of genome position, reference, mutation, reference supporting reads and variant supporting read. Will appreciate suggestion regarding suitable language for it.

Regards,
Seema
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Old 03-05-2014, 04:27 AM   #2
TiborNagy
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I think you would like to create a VCF-like file (from a VCF file?). If this is the case Awk/Perl/Python is the suitable language.
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Old 03-05-2014, 05:41 PM   #3
bi_maniac
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If you post an example, I could help you. I am new in Bioinformatics but seasoned in computers
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Old 03-06-2014, 12:41 AM   #4
seema12345
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Quote:
Originally Posted by bi_maniac View Post
If you post an example, I could help you. I am new in Bioinformatics but seasoned in computers
Hi,

Attaching a sample data...column 1, 2, 3, 4, 5 are genome position of bases, reference, mutation, reference supporting read and variant supporting read, respectively.
I need to get reverse complement of both reference and mutation column.
The output will be exactly like this format...just the bases in reference and mutation column will be reverse complement ..

data:
2153889 T 12 0
2153890 C +G 11 1
2153891 A -G 11 1
2153892 G +T 10 1
2153893 C +A 11 1

I am trying to write the code in perl-shell script..
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Old 03-07-2014, 07:00 PM   #5
bi_maniac
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Default I see here two issues: computer programming and bioinformatics ...

... I mean: I have no problems with perl script.
I do not know the meaning of those "+" and "-" signs.
Please correct me if I am wrong.

Last edited by bi_maniac; 03-07-2014 at 07:02 PM.
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