genome_mapping_using_bowtie2

genome_mapping_using_bowtie2.bash

sudo apt install bowtie2

mkdir ce_idx
bowtie2-build --threads 4 ref/GCF_000002985.6_WBcel235_genomic.fna ce_idx/idx

ls ce_idx/
# idx.1.bt2  idx.2.bt2  idx.3.bt2  idx.4.bt2  idx.rev.1.bt2  idx.rev.2.bt2

more reads/SRR27482193/SRR27482193_1.fastq | grep "@SRR27482193" | wc -l
# 4516699

more reads/SRR27482193/SRR27482193_2.fastq | grep "@SRR27482193" | wc -l
# 4516699

mkdir maps
bowtie2 -p 4 -x ce_idx/idx \ 
-1 reads/SRR27482193/SRR27482193_1.fastq \
-2 reads/SRR27482193/SRR27482193_2.fastq \
-S maps/bt2.global.sam >& maps/bt2.global.log

bowtie2 -p 4 -x ce_idx/idx \
-1 reads/SRR27482193/SRR27482193_1.fastq \
-2 reads/SRR27482193/SRR27482193_2.fastq \
-S maps/bt2.local.sam 
--local >& maps/bt2.local.log