References: Host

Host (Human)

The host used in the example will be the HG38 human genome reference. If you are working with other host organism you can follow the following steps with its reference genome.

Create a directory named HUMAN_GENOME_REFERENCES/ and go inside it.

[Whole Genome] (http://hgdownload.cse.ucsc.edu/goldenPath/hg38/bigZips/analysisSet/)

1. Create a directory HUMAN_GENOME_REFERENCES/WG/ and go inside it.

2. Download the 2bit file. We use this file because it contains the processed sequence ready to use in analysis pipelines.

   wget http://hgdownload.cse.ucsc.edu/goldenPath/hg38/bigZips/hg38.analysisSet.2bit' > hg38.2bit

   WARNING! This step will download a relatively file. Before executing this command please make sure you have sufficient storage space.

3. Convert from 2bit to fasta with [twobittofasta] (https://genome.ucsc.edu/goldenpath/help/twoBit.html)

   twoBitToFa hg38.2bit hg38.fa

4. Create Bowtie2 genome index

`bowtie2-build REFERENCES/HUMAN_GENOME_REFERENCE/WG/hg38.fa REFERENCES/HUMAN_GENOME_REFERENCE/WG/bwt2/hg38.AnalysisSet`