Apologies if this is somewhat basic - I usually work with smaller genomes and use local custom genome data viewers but now I have to work with some mammalian genomes and this is all new to me.
I simply want to visualize RNA-seq read coverage of my samples on the Ensembl genome browser. I understand that I can't upload a huge bam file but actually all I need is coverage plots for several samples, not the full alignments. I also don't need the whole genome - I mainly need to check a few gene regions.
To my surprise I so far failed to find out how others do this. What I have done now is to use samtools "depth" to get the coverage data for a region of interest from my bam file and then to convert that into WIG format using a custom Perl script. This works for a single sample but so far I couldn't get it to work if I want to combine coverage data for several samples into one track.
Here is a little toy example that does add two tracks and they are both plotted in the Ensembl mouse genome browser when I upload them as WIG but they are on top of each other although two separate y axis are drawn (but only one is used). Here is the wig file:
track type=wiggle_0 name="track-1" description="track 1" visibility=full autoScale=off viewLimits=0:25 color=50,150,255 priority=1 graphType="bar" variableStep chrom=X span=100 74007187 10 74007287 20 74007487 5 74007687 13 variableStep chrom=X span=10 74007787 20 74007797 25 74007807 10 74007827 20 track type=wiggle_0 name="track-2" description="track 2" visibility=full autoScale=off viewLimits=0:25 color=0,200,100 priority=2 graphType="bar" fixedStep chrom=chr19 start=49307401 step=300 span=200 variableStep chrom=X span=100 74007187 3 74007287 15 74007387 24
I guess I have two questions:
- how can I get this to display so that both tracks are visible (preferably with a single wig file like I have tried here) - is there a way to make them overlay transparetly or to force them being plotted on the two different y axes?
- am I doing something silly to being with? How do others visualise RNAseq data on Ensembl if you don't have a server to host your bam files? That must be a common problem, right?
Thanks for your help!