Hi all, I am using bwa mem in this pipeline
bwa mem -t 12 -M -B 4 ref.fas xxx.r1.fastq.gz xxx.r1.fastq.gz > xxx.sam samtools view -h -b -S -@ 11 xxx.sam > xxx.bam samtools sort xxx.bam > xxx.sorted.bam samtools depth xxx.sorted.bam > xxx.bed
Then with R, I read the bed file as dataframe and I plot the data. I get very low depth and a plot that is really fluctuating.
does anybody know if there is a way to improve the depth? thanks a lot for any help.