Reference Genome

#Reference Genome Obtain a reference genome from iGenomes. In this example analysis we will use the human hg19/NCBI build 37 version of the genome
In this tutorial we are actually going to perform the analysis using only a single chromosome (chr22) to make it run faster...

Create the necessary working directory

cd $RNA_HOME
mkdir refs
mkdir refs/hg19/
mkdir refs/hg19/fasta/
mkdir refs/hg19/fasta/22/
cd refs/hg19/fasta/22/

Make a copy of chr22 fasta from the CourseData directory to your working directory The complete data from which these files were obtained can be found at: http://cufflinks.cbcb.umd.edu/igenomes.html You could use wget to download the Homo_sapiens_Ensembl_GRCh37.tar.gz file (under Homo sapiens -> Ensembl -> GRCh37), then unzip/untar This has been done for you and that data placed in /media/cbwdata/CourseData/RNA_data/

wget https://xfer.genome.wustl.edu/gxfer1/project/gms/testdata/bams/colon_tumor_vs_normal/downsampled_10pc_chr22/22.fa

View the first 10 lines of this file

head 22.fa

How many lines and characters are in this file?

wc 22.fa

To get all chromosomes instead of just chr22 you could do the following:

cd $RNA_HOME
mkdir -p refs/hg19/fasta/
cd refs/hg19/fasta/
cp /media/cbwdata/CourseData/RNA_data/iGenomes/Homo_sapiens/Ensembl/GRCh37/Sequence/Chromosomes/* .
cat *.fa > hg19.fa

Note: Instead of the above, you might consider getting reference genomes and associated annotations from UCSC
e.g., ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/chromosomes/
Wherever you get them from, the names of your reference sequences (chromosomes) must those matched in your annotation gtf files.