I want to visualise insert sizes in my mate-pair library and calculate statistics like mean, standard deviation..
I have found this tool http://blog.malde.org/posts/bamstats.html that makes beautiful graphs like the one above (the plot shows mate pair library - green - contaminated by paired end reads in red).
However, based on output of this program it seems that there are plenty of paired-end reads in my library and only few mate-pairs (orientation outwards, outies on the plot). I want to verify this with another tool. Picard's CollectInsertSizeMetrics works only for paired-end reads according to manual. What are other possibilities?
Moreover, I got pretty wild statistics from bamstats package, probably because of outliers in my data:
#Alignment count prop mean stdev skew kurt innies 11853 33.53% 861169.9 8776007.0 12.2 161.7 outies 4560 12.90% 2644111.4 15288468.3 6.7 46.7 lefties 4681 13.24% 2769622.5 16057397.2 6.4 42.8 righties 4585 12.97% 3128289.8 17007034.4 6.2 39.5
Any suggestions are welcome. I need three things: estimated mean (after removal of outliers), standard deviation (again after removal of outliers) and visualisation. Both, histograms and boxplots work for me.
Thanks a lot!