Hi Qinglu I suspect these two plots are loaded into Artemis as user plots. So they probably generated the plot data with scripts and loaded them via the Graph menu as user plots.
For the strand-specific plot you could generate this via the BAM view by separating the strands into separate BAM files, using samtools: Forward: samtools view -bF 0x10 inFile.bam > inFileFwd.bam Reverse: samtools view -bf 0x10 inFile.bam > inFileBwd.bam Load the forward and reverse BAM files and when you right click on the BAM panel and from the Graph menu select Coverage they will be plotted separately. Regards Tim On 2/26/12 2:29 AM, "Qinglu Zeng" <qin...@mit.edu> wrote: > Hi Tim, > I have two questions: > > 1. I want to compare different RNA-seq libraries. How can I normalized the > coverage to the sequencing depth of each library? Oliver et al (2009 BMC > Genomics) did this in Figure 2, but I could not figure out how to do it. > > 2. How to show a strand-specific coverage plot as Croucher et al (2010 Curr > Opin > Microbiol) showd in Figure 2d? > > Thanks! > > Qinglu _______________________________________________ Artemis-users mailing list Artemis-users@sanger.ac.uk http://lists.sanger.ac.uk/mailman/listinfo/artemis-users
