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I think we count a multi-base indel only once when subtracting the indels from the edits to obtain mismatches
https://github.com/fulcrumgenomics/fgprimer/blob/6cf2542e927ced37dd0dce4c335de8dff07789c7…
nh13 updated
4 months ago
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~/RDPTools/PrimerDesign/dist$ ls
PrimerDesign.jar
RDPTools/PrimerDesign/dist$ pwd
~/RDPTools/PrimerDesign/dist$ cd
$ java -Xmx8g -jar /home/eesi/RDPTools/PrimerDesign/dist/PrimerDesign.jar --help…
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Hi,
I am having the following issue. Any help will be appreciated.
A problem with the BLAST results file /primerdesign/Lactobacillus_curvatus/Pangenome/results/primer/primerblast/primer_0_result…
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Start searching primer for Bacillus_subtilis
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fatal error while working on Bacillus_subtilis check logfile /home/cberruto/speciesp…
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eesi@dhantha-CG1330:~/Desktop$ java -jar /home/eesi/RDPTools/PrimerDesign/dist/PrimerDesign.jar -subcommand select -input /home/eesi/Desktop/reduced.mfa -SlidingScale true -productLengthMin 150 -produ…
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Hi,
When I run or rerun speciesprimer (on a docker container with 15.51 gb RAM allocated to it) a single results file is not successfully created. I can not determine from the logs what the problem…
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I am using the example file from previous issue that you had uploaded (exampleVar.txt) and config file as described using hg19 fasta i get this error
2017-05-16 17:18:11.326957 Primers to test: 0…
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“”“download-ivy:
[mkdir] Created dir: /root/.ant/lib
[get] Getting: http://repo2.maven.org/maven2/org/apache/ivy/ivy/2.1.0-rc2/ivy-2.1.0-rc2.jar
[get] To: /root/.ant/lib/ivy.jar
…
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(args_oap) lishuxian@tong1:/mnt/md0/LSX$ ~/primerdesign/PMPrimer/pmprimer.py -f modified.fasta -p notsameseq -a muscle threshold:0.50 merge primer2 --debuglevel 1
序列集共有序列 144 条 / Number Of Sequece…
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Hi there,
Thanks for this great container, very helpful.
However, I have some troubles at species and pathovars level.
1) I need primers for a particular bacterial species. There are 14 genomes a…