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bioinfo-ut / PlasmidSeeker

A k-mer based program for the identification of known plasmids from whole-genome sequencing reads
BSD 3-Clause "New" or "Revised" License
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-i [your WGS sample FASTQ file], is it paired or unpaired fastq file? #21

Closed ilkaybuysal closed 4 years ago

ilkaybuysal commented 4 years ago

For running plasmidseeker, we need to provide the fastq file, but I'm not sure if we should provide both R1 and R2 or the unpaired.fq file? perl plasmidseeker.pl -d [your database dir] -i [your WGS sample FASTQ file] -b [close reference bacterium FASTA file] -o [output file name]

mihkelvaher commented 4 years ago

As the copy numbers are estimated using coverages, it's better to ensure good coverage as there are more fluctuations with low coverage. I'd suggest merging all of the fastq files. Read pairing is not taken into account.

ilkaybuysal commented 4 years ago

THanks a lot for your answer! So I should merge MG.R1 and MG.R2 and use it as the input?

mihkelvaher commented 4 years ago

Yes.

ilkaybuysal commented 4 years ago

Thanks a lot!