##GTR lset applyto=() nst=6 # GTR lset applyto=() nst=6 rates=propinv # GTR + I lset applyto=() nst=6 rates=gamma # GTR + gamma lset applyto=() nst=6 rates=invgamma # GTR + I + gamma
##SYM
lset applyto=() nst=6 # SYM
prset applyto=() statefreqpr=fixed(equal)
| for row in $(cat nucmer.coords | awk -v OFS=, '{if ($10 == 100.00 && $11 == 100.00 && $7 == 100.00 && $12 != $13) {print $12,$13}}') | |
| do | |
| echo $row | tr ',' '\n' | sort | tr '\n' ',' | sed 's/,$//' | |
| echo | |
| done | cut -d, -f2 | sort -u > duplicatecontigs.txt |
| use strict; | |
| use warnings; | |
| use Text::CSV_XS; | |
| use Data::Printer; | |
| my $csv = Text::CSV_XS->new({ binary => 1, sep_char => "\t" }); | |
| open my $fh, "<", $ARGV[0] or die $!; | |
| open my $fh2, "<", $ARGV[1] or die $!; | |
| # 1. 키맵 생성 |
| use strict; | |
| use warnings; | |
| use Text::CSV_XS; | |
| use Data::Printer; | |
| my $csv = Text::CSV_XS->new({ binary => 1, sep_char => "\t" }); | |
| open my $fh, "<", $ARGV[0] or die $!; | |
| open my $fh2, "<", $ARGV[1] or die $!; | |
| # 1. 키맵 생성 |
| #!/bin/bash | |
| # bash generate random alphanumeric string | |
| # | |
| # bash generate random 32 character alphanumeric string (upper and lowercase) and | |
| NEW_UUID=$(cat /dev/urandom | tr -dc 'a-zA-Z0-9' | fold -w 32 | head -n 1) | |
| # bash generate random 32 character alphanumeric string (lowercase only) | |
| cat /dev/urandom | tr -dc 'a-zA-Z0-9' | fold -w 32 | head -n 1 |
MAKER is a great tool for annotating a reference genome using empirical and ab initio gene predictions. GMOD, the umbrella organization that includes MAKER, has some nice tutorials online for running MAKER. However, these were quite simplified examples and it took a bit of effort to wrap my head completely around everything. Here I will describe a de novo genome annotation for Boa constrictor in detail, so that there is a record and that it is easy to use this as a guide to annotate any genome.