Hi to everybody,
I am in the process of finishing my Contigs to a complete sequence and try to use ABACAS to assist me in gap closure. I want ABACAS to take over the primer design for me but it refuses to put out primer sequences. The tool runs as expected, MUMMER and Primer3 are installed and should be in $PATH. ABACAS creates the primer files (which are empty) and doesn't report errors in the primer design problem:
"Please wait... extracting target regions ...
26 gaps found in target sequence
Please wait...
Looking for primers...
Running Primer3 and checking uniquness of primers...
Counting left and right primer hits from a nucmer mapping (-c 15 -l 15)
PRIMER DESIGN DONE"
On Biostars someone had similar problems but nobody posted a solution to it. Did someone had similar issues and found a solution? Is something wrong with my Primer3?
Also: Everything else seems to work fine. I get reference maps and can view annotated version in ACT.
Thanks,
I am in the process of finishing my Contigs to a complete sequence and try to use ABACAS to assist me in gap closure. I want ABACAS to take over the primer design for me but it refuses to put out primer sequences. The tool runs as expected, MUMMER and Primer3 are installed and should be in $PATH. ABACAS creates the primer files (which are empty) and doesn't report errors in the primer design problem:
"Please wait... extracting target regions ...
26 gaps found in target sequence
Please wait...
Looking for primers...
Running Primer3 and checking uniquness of primers...
Counting left and right primer hits from a nucmer mapping (-c 15 -l 15)
PRIMER DESIGN DONE"
On Biostars someone had similar problems but nobody posted a solution to it. Did someone had similar issues and found a solution? Is something wrong with my Primer3?
Also: Everything else seems to work fine. I get reference maps and can view annotated version in ACT.
Thanks,
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