Once you have cleaned paired end reads, map them to a reference using BWA
map reads
#start idev session if you haven't idev #copy over the exercise directory cds cd rad_intro cp -r /work/02260/grovesd/lonestar/intro_to_rad_2017/mapping/mapping_ddRAD_bwa . cd mapping_ddRAD_bwa #look at sample fastqs ls -l *.fq #we have 3 sets of paired end reads #check our reference #(we're using just chromosome3 to keep things fast) less stickleback_chrom3.fasta #load the BWA module module load bwa #build a BWA index for our reference bwa index stickleback_chrom3.fasta #look at the documentation for bwa mem bwa mem #map the reads to the indexed reference bwa mem stickleback_chrom3.fasta sampleA_r1.fq sampleA_r2.fq > sampleA.sam bwa mem stickleback_chrom3.fasta sampleB_r1.fq sampleB_r2.fq > sampleB.sam bwa mem stickleback_chrom3.fasta sampleC_r1.fq sampleC_r2.fq > sampleC.sam #look at results ls -l *.sam #sam files are human readable, but take up large amounts of space #bam files take up less space and are faster to read #so we should convert the sam files to bams and sort them. #We will do this with samtools #load the samtools module module load samtools #convert to bam and sort samtools view -b sampleA.sam | samtools sort -o sampleA.sorted.bam samtools view -b sampleB.sam | samtools sort -o sampleB.sorted.bam samtools view -b sampleC.sam | samtools sort -o sampleC.sorted.bam #note the size difference between sams and bams ls -lh *.sam ls -lh *.bam #Note that all of that could have been done in single command eg: bwa mem stickleback_chrom3.fasta sampleA_r1.fq sampleA_r2.fq | samtools view -b | samtools sort -o sampleA.sorted.bam
