Generating input file for Primer3 using p3

Generating input file for Primer3 using p3_in.pl (MISA)

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4.6 years ago

evoclive • 0

Hello all

I am using a published genome to develop SSR primers (secondary question: is this possible from a single published genome?). I have run MISA to identify microsatellites and their locations. I believe the next step is to use 'p3_in.pl' to convert the *.misa file to something readable for Primer3. However, when I type:

p3_in.pl myMisaFile.misa

I get an empty output and an error: Use of uninitialized value $count in concatenation (.) or string at p3_in.pl line 34, <SRC> chunk 25.

My reference genome Fasta headers are simple with no spaces, e.g. '>chr01'

Any help please

Best wishes

Clive

Primer3 MISA SSR • 1.7k views

ADD COMMENT • link 4.6 years ago by evoclive • 0

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What are the versions of the programs (MISA and Primer3)? MISA 1.0 do not work with Primer3 version 2, it needs Primer 3 version 1 - I am sure it works with Primer3 version 1.1.4.

ADD REPLY • link 4.6 years ago by h.mon 35k

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I installed P3 v1.14 - but I don't understand why I get no output from p3_in.pl before running Primer3. Or is it possible to run P3 v1.1.4 on *.misa files?

ADD REPLY • link 4.6 years ago by evoclive • 0

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