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I think there is a hard coded path that you missed, and may want to correct for the public release:
lib/draw_circos_images.sh
cdsDdbbFile="/processing_Data/bioinformatics/research/20160530_ANTIB…
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In the genomes list for Brucella inopinata BO1, it has 55 contigs listed in the table, but when you highlight that row, in the information panel it says there are 48 sequences:
Then when I go to …
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I've been doing plasmid-enriched MinION read assemblies and I understand that Canu causes a terminal repeat, which I can easily cut out.
However, I've been having problems with non-terminal direct …
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I would think we want to cover isolation, activation, culture (pre- and post-activation), and proliferation assays for sure. Do we want to cover electroporation of plasmids, mRNA, and RNPs? Experience…
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```
pip3 install mob_typer
mob_typer -o mob1 -i NC_003197.fasta -n 18
ERROR:root:Error needed database missing "/home/linuxbrew/.linuxbrew/lib/python3.7/site-packages/mob_suite/databases/rep.dn…
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Currently, patlasflow outputs a JSON for each contig in each sample. I suggest merging the individual contig JSONs into a single file, with a key:value pair for each contig:plasmids.
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canu 1.7 "Ensure[s] that every raw read is either corrected or used as evidence for correcting some other raw read. This serves to rescue short plasmids in high coverage datasets, and it is no longer …
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The following genomes lack a number in the "Sequences" field
{"id_list":{"genome_id":["1496.2589","1496.2590","1496.2592","1496.2593","1496.2595","1496.2594","1496.2591","1496.2598","1496.2597","14…
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Hey Smaegol,
Thanks for updating the installation for PlasFlow. I am excited to use this novel tool to search for plasmids but ran into the following trying to install the new updates:
Any t…
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Hello,
I am looking for the copy number of the plasmid pHNSHP45 in E.coli isolates. The plasmid should be present. However, it was not identified by plasmidseeker. Therefore, I was wondering whether …