PCR Primer Extraction

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dpaetkau
Posts: 31
Joined: Fri Jun 05, 2009 6:18 pm

PCR Primer Extraction

Post by dpaetkau » Tue Sep 23, 2014 2:01 pm

Hello All,

I am having trouble using the aceNOligos.perl line to extract PCR primers from the ace file. (where N = latest ace file number).
So, here is what I did.
Opened DBIA1412001 in consed.
Located the low consensus quality region at about 23100 (I chose this as an example and don't really care if it can be fixed another way).
I followed the primer picking steps (Pick Top Strand- First PCR Primer, then Pick Bottom Strand, etc)
I saved the assembly as ./DBIA1412001.ace.3.
Navigated to Tag-Oligos to make sure they existed - they are at 22666-22688 and 23170-23190.
Closed Consed and tried all of the following in the command line:
ace3Oligos.perl
DBIA1412001.ace.3Oligos.perl
ace.3.Oligos.perl
and any other combination that I could think of (see attached picture).
I keep getting the file not found error.

I have noticed that students are making mistakes when they are typing in their Oligos from the Tag label windows, so I would really like them to copy and paste.

Any ideas how to fix this problem.

Don
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wleung
Posts: 185
Joined: Sun Feb 04, 2007 7:41 pm
Location: Washington University in St. Louis

Re: PCR Primer Extraction

Post by wleung » Tue Sep 23, 2014 3:12 pm

The name of the program is ace2Oligos.perl and the syntax for the command is as follow:

Code: Select all

ace2Oligos.perl <name of ace file> <name of oligos file>
Therefore, you can use the following command to extract the oligos in DBIA1412001.ace.3:

Code: Select all

ace2Oligos.perl ./DBIA1412001.ace.3 ./pcr_primers.txt
If the command is successful, you will find the list of oligos in the file pcr_primers.txt in the current directory (i.e., inside edit_dir).

dpaetkau
Posts: 31
Joined: Fri Jun 05, 2009 6:18 pm

Re: PCR Primer Extraction

Post by dpaetkau » Tue Sep 23, 2014 5:01 pm

Thank you Wilson,

Now that I look back at the command, I see my very silly mistake. I appreciate you putting up with all of our silly questions.

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