IndexFA

Create .fai index file for custom genome

In order to use a custom genome on the IGV Web App, you must create a fasta index file (.fai) from the FASTA file available on NBCI.

##Step 1: Download FASTA genome from NCBI and upload to workspace
##Step 2: Rename to something simple (BacCoag.fa in example)
##Step 3: Install and seqTools
library(seqTools)

## Loading required package: zlibbioc

##Step 4: Use writeFai function to produce index file.  Make sure output file name is exactly the same plus .fai.
writeFai("BacCoag.fa", "BacCoag.fa.fai")

## [write_fai] File ( 1/1)    1 sequences           70 total length.

## [write_fai] done.

#read in file and print to show format (SKIP FOR ASSIGNMENT)
myData <- read.table('BacCoag.fa.fai',sep="\t")
myData

##                                                                             V1
## 1 >NZ_CP011939.1 Weizmannia coagulans strain S-lac chromosome, complete genome
##   V2 V3 V4 V5
## 1 70 77 70 71