Open ghost opened 3 years ago
Hi. Yes, it works with minimap2. However, I've never gotten around to test parameters for minimap2, so I can't say anything about sensitivity, etc. But you can use it with minimap2 like this for example.
/path/to/minidot -M /path/to/minimap2 -m "-x asm20" prochlorococcus.fa
Hello! I have minimap2, so I use bin/minidot -M path2/minimap2 -m "-x asm20" -o Canu_Flye_full.pdf Canu_PacBio.fasta Flye_PacBio.fasta
But, there's some error in R [14:43:30] /linuxhome/tmp/jose/minimap2/minimap2 .. ok [14:43:30] samtools .. ok [14:43:30] prepping .. done [14:43:30] mode: -x asm20 ( bp) "-x asm20" [14:43:30] mapping .. done [14:44:47] plotting Error in scan(file = file, what = what, sep = sep, quote = quote, dec = dec, : line 2 did not have 18 elements Calls: read.table -> scan Execution halted failed
Thanks
It should because both return PAF... Can you run minimap2 -x asm20 Canu_PacBio.fasta Flye_PacBio.fasta
to see if you get proper output (and maybe post that?)
On February 8, 2022 2:46:44 PM GMT+01:00, botellaflotante @.***> wrote:
Hello! I have minimap2, so I use bin/minidot -M path2/minimap2 -m "-x asm20" -o Canu_Flye_full.pdf Canu_PacBio.fasta Flye_PacBio.fasta
But, there's some error in R [14:43:30] /linuxhome/tmp/jose/minimap2/minimap2 .. ok [14:43:30] samtools .. ok [14:43:30] prepping .. done [14:43:30] mode: -x asm20 ( bp) "-x asm20" [14:43:30] mapping .. done [14:44:47] plotting Error in scan(file = file, what = what, sep = sep, quote = quote, dec = dec, : line 2 did not have 18 elements Calls: read.table -> scan Execution halted failed
Thanks
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this is what I get that way. I just renamed to .txt to upload here canu_flye.txt y
Hello!
question in the tittle, since minimap is "deprecated".
Thank you