3.genome

Indexes for Bowtie2 and genome in FASTA format

This folder will contain the Bowtie Indexes and genomes in FASTA format.

We download them from igenome from Illumina.

H. sapiens, NCBI GRCh38

Bowtie 2 Genome - H. sapiens, NCBI GRCh38

• http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml

wget ftp://igenome:G3nom3s4u@ussd-ftp.illumina.com/Homo_sapiens/UCSC/hg38/Homo_sapiens_UCSC_hg38.tar.gz

Need to tar -zxvf AND remove some folders (BWA, etc...) to save som space

tar -zxvf Homo_sapiens_UCSC_hg38.tar.gz

Remove annotation folder

cd Homo_sapiens/UCSC/hg38/
rm -rf Annotation/

Remove unnecessary Indexes

cd Sequence/
rm -rf BowtieIndex/ BWAIndex/ Chromosomes/
cd ../../../../

Remove TAR.GZ file

cd /absolute/path/to/remap-pipeline/3.genome/
rm -f Homo_sapiens_UCSC_hg38.tar.gz #-- Clean if you wabt
rm README.txt  #-- Ilumina README

A. thaliana, TAIR10

Bowtie 2 Genome - Arabidopsis thaliana TAIR10

• http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml

wget ftp://igenome:G3nom3s4u@ussd-ftp.illumina.com/Arabidopsis_thaliana/Ensembl/TAIR10/Arabidopsis_thaliana_Ensembl_TAIR10.tar.gz 
wget ftp://igenome:G3nom3s4u@ussd-ftp.illumina.com/Arabidopsis_thaliana/NCBI/TAIR10/Arabidopsis_thaliana_NCBI_TAIR10.tar.gz

Need to tar -zxvf AND remove some folders (BWA, etc...) to save som space

tar -zxvf Arabidopsis_thaliana_NCBI_TAIR10.tar.gz

Remove annotation folder

cd Arabidopsis_thaliana/NCBI/TAIR10/
rm -rf Annotation/

Remove unnecessary Indexes

cd Sequence/
rm -rf BowtieIndex/ BWAIndex/ Chromosomes/
cd ../../../../

Remove TAR.GZ file

rm Arabidopsis_thaliana_Ensembl_TAIR10.tar.gz Arabidopsis_thaliana_NCBI_TAIR10.tar.gz
rm README.txt  #-- Ilumina README