Will it work properly with minimap2 output
Opened this issue · 4 comments
Hello!
question in the tittle, since minimap is "deprecated".
Thank you
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
this is what I get that way. I just renamed to .txt to upload here
canu_flye.txt
y