search

thackl / minidot

Fast and pretty dotplots for whole genomes assemblies using minimap and R/ggplot2
MIT License
74 stars 10 forks source link

Will it work properly with minimap2 output #12

Open ghost opened 4 years ago

ghost commented 4 years ago

Hello!

question in the tittle, since minimap is "deprecated".

Thank you

thackl commented 4 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
botellaflotante commented 2 years ago

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

thackl commented 2 years ago

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

-- Reply to this email directly or view it on GitHub: https://github.com/thackl/minidot/issues/12#issuecomment-1032626986 You are receiving this because you commented.

Message ID: @.***>

botellaflotante commented 2 years ago

this is what I get that way. I just renamed to .txt to upload here canu_flye.txt y