Reference Genome

#1-ii. Reference Genomes Obtain a reference genome from iGenomes. In this example analysis we will use the human hg19/NCBI build 37 version of the genome. Furthermore, we are actually going to perform the analysis using only a single chromosome (chr22) and the ERCC spike-in 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/chr22_ERCC92/
cd refs/hg19/fasta/chr22_ERCC92/

Make a copy of chr22 + ERCC fasta in your working directory. The complete data from which these files were obtained can be found at: http://cole-trapnell-lab.github.io/cufflinks/igenome_table/index.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 on an ftp server. It contains chr22 and ERCC transcript fasta files in both a single combined file and individual files. Download them now.

wget http://genome.wustl.edu/pub/rnaseq/data/brain_vs_uhr_w_ercc/downsampled_5pc_chr22/chr22_ERCC92.tar.gz
tar -zxvf chr22_ERCC92.tar.gz
rm chr22_ERCC92.tar.gz

View the first 10 lines of this file

head chr22_ERCC92.fa

How many lines and characters are in this file?

wc chr22_ERCC92.fa

View 10 lines from approximately the middle of this file

head -n 425000 chr22_ERCC92.fa | tail

Note: Instead of the above, you might consider getting reference genomes and associated annotations from UCSC. e.g., http://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 (described in the next section).

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