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:

 samtools view -bF 0x10 inFile.bam > inFileFwd.bam

 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


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

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