| # Get a list of all organisms | |
| curl -s "http://rest.kegg.jp/list/organism" > organisms-all.txt | |
| # Get just a few of interest | |
| cat organisms-all.txt | awk '$2~/^(hsa|mmu|rno|cfa|bta|gga|xla|xtr|dre|dme|cel|ath|ehi|tgo|eco|sau|mtu|mav|cje|ccol)$/' > organisms-of-interest.txt | |
| # Get the accession codes for each | |
| cut -f1 organisms-of-interest.txt > organisms-of-interest-codes.txt | |
| # Make a directory to put all the kgml files downloaded |
| Go to github | |
| Create new repository [don't need to initialize with the readme (can add later)] | |
| Go to R Studio | |
| File -> New Project -> Version Control -> Git | |
| Ctrl+V repository URL from GitHub | |
| File -> New -> Markdown, enter Title, etc. | |
| In the Markdown window, change "output=html_document" to "output=github_document" | |
| Knit the document for the first time, will prompt you to save | |
| Save as Title.rmd | |
| In the "git" tab of the R studio Environment window, you will notice that the knit produced: |
| # see below for UPDATES that include more shorter ways of conversions | |
| # How to convert GTF format into BED12 format (Human-hg19)? | |
| # How to convert GTF or BED format into BIGBED format? | |
| # Why BIGBED (If GTF or BED file is very large to upload in UCSC, you can use trackHubs. However trackHubs do not accept either of the formats. Therefore you would need bigBed format) | |
| # First, download UCSC scripts | |
| wget http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/gtfToGenePred | |
| wget http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/genePredToBed | |
| wget http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bedToBigBed |
##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)