mapping_covidSeq

#This is used to map raw fastq files to SARS-CoV-2 genome
#Sample code:
bowtie2 -x ../NC_045512_INDEX -q -1 fastq/20210524-CovidSeq1-S1_S1_L001_R1_001.fastq.gz -2 fastq/20210524-CovidSeq1-S1_S1_L001_R2_001.fastq.gz -S mapped/20210524-CovidSeq1-S1_S1.sam 

#batch script as follows:

awk '{print "bowtie2 -x ../NC_045512_INDEX -q -1 fastq/"$1"_L001_R1_001.fastq.gz -2 fastq/"$1"_L001_R2_001.fastq.gz -S mapped/"$1".sam 2> log_files/bowtie_log_"$1".txt"}' ./meta/SRX.list > scripts/bowtie2_covidSeq.sh
chmod 755 ./scripts/bowtie2_covidSeq.sh
nohup ./scripts/bowtie2_covidSeq.sh > log_files/bowtie2_covidSeq.log &

#next step will be to generate bam files from the sam files 
#sort the bam files 
#and index the bam files 

#sample code for doing the indexing and mapping:

samtools view -S -b mapped/20210524-CovidSeq1-S1_S1.sam > ./bam_files/20210524-CovidSeq1-S1_S1.bam
samtools sort ./bam_files/20210524-CovidSeq1-S1_S1.bam -o ./sorted_bam/20210524-CovidSeq1-S1_S1.sorted.bam
samtools index ./sorted_bam/20210524-CovidSeq1-S1_S1.sorted.bam

Generate respectiev batch scripts for that:
awk '{print "samtools view -S -b mapped/"$1".sam > ./bam_files/"$1".bam"}' ./meta/SRX.list > scripts/samtobam.sh
awk '{print "samtools sort ./bam_files/"$1".bam -o ./sorted_bam/"$1".sorted.bam"}' ./meta/SRX.list > scripts/sort_bam.sh
awk '{print "samtools index ./sorted_bam/"$1".sorted.bam"}' ./meta/SRX.list > scripts/index_bam.sh

chmod 755 ./scripts/samtobam.sh
chmod 755 ./scripts/sort_bam.sh
chmod 755 ./scripts/index_bam.sh

nohup ./scripts/samtobam.sh > log_files/samtobamq.log &
nohup ./scripts/sort_bam.sh > log_files/sort_bam.log &
nohup ./scripts/index_bam.sh > log_files/index_bam.log &