Reference Genome

#1-ii. Reference Genomes

Obtain a reference genome from iGenomes. In this example analysis we will use the human GRCh38 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 $RNA_HOME
export REF_BASE=/home/ubuntu/workspace/data/fasta/GRCh38/chr22_with_ERCC92
export REF_FASTA=${REF_BASE}.fa
echo $REF_FASTA

The complete data from which these files were obtained can be found at: ftp://ftp.ensembl.org/pub/release-85/fasta/homo_sapiens/dna/. You could use wget to download the Homo_sapiens.GRCh38.dna_sm.primary_assembly.fa.gz file, then unzip/untar.

This has been done for you and that data placed on your AWS instance. It contains chr22 and ERCC transcript fasta files in both a single combined file and individual files.

cd /home/ubuntu/workspace/data//fasta/GRCh38/
ls 

View the first 10 lines of this file

head $REF_FASTA

How many lines and characters are in this file?

wc $REF_FASTA

View 10 lines from approximately the middle of this file

head -n 425000 $REF_FASTA | 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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