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oschwengers / platon

Identification & characterization of bacterial plasmid-borne contigs from short-read draft assemblies.
https://doi.org/10.1099/mgen.0.000398
GNU General Public License v3.0
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The number of contigs in plasmid.fasta is not the same as the number of contigs in .tsv #28

Closed xuanji2017 closed 2 years ago

xuanji2017 commented 2 years ago

Hi, I found that the number of contigs in plasmid.fasta is not the same as the number of contigs in .tsv. The number of contigs in my .tsv file is 112,598 but the number of contigs in plasmid.fasta is 111,936. Do you have any idea what the problem is? which one should I use? And also the contig number in plasmid.fasta+ the contig number in chromosome.fasta < the total number of the contigs. What are the others? Thanks a lot!

Best Xuanji

oschwengers commented 2 years ago

Hi @xuanji2017, thanks for reporting. This seems rather odd and has not been reported so far. Due to the large number of contigs I infere that this is a metagenome assembly? Could you provide more information like the executed version, parameters, options, etc? The log file would certainly help to figure out what happened (maybe GNU zipped?)

oschwengers commented 2 years ago

Hi @xuanji2017 , is this still active? Otherwise, I'd close this for now.

xuanji2017 commented 2 years ago

yes, please. Thanks lot!

Xuanji Li postdoc

University of Copenhagen Faculty of Science Section for Microbiology Universitetsparken 15, bldg. 1 DK2100 Copenhagen

+45 71401828

From: Oliver Schwengers @.***> Sent: 29 March 2022 08:50:27 To: oschwengers/platon Cc: Xuan Ji Li; Mention Subject: Re: [oschwengers/platon] The number of contigs in plasmid.fasta is not the same as the number of contigs in .tsv (Issue #28)

Hi @xuanji2017https://eur02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fxuanji2017&data=04%7C01%7Cxuanji%40bio.ku.dk%7C42ee87d8e85641b187ef08da11506983%7Ca3927f91cda14696af898c9f1ceffa91%7C0%7C0%7C637841334309703486%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=y5Ay9mpThV4GMcc4vFqS2LWCMYQJzTro8TJ6yWvkjFc%3D&reserved=0 , is this still active? Otherwise, I'd close this for now.

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