I'm trying to map fastq files from bacterial RNA-seq studies and then view the bam files in Artemis using the coverage by strand or strand stack view. However, in the few paired-end examples I tried from the SRA, I just get reads mapping almost equally to both strands, so the coverage looks like a mirror image. I also tried Rockhopper and the plus and minus tracks look right, but I would like to know how I can fix this code below. Thanks.
bowtie2-build NC_003143.fna yp
bowtie2 -p 4 -x yp -1 SRR1041589_1.fastq -2 SRR1041589_2.fastq | samtools view -bS - | samtools sort - tmh
samtools index tmh.bam
art -Dbam=tmh.bam NC_003143.gbk
# select views-> coverage by strand