Question: Visualize Insert Size For Mate-Pairs And Calculate Statistics
gravatar for Biomonika (Noolean)
3.7 years ago by
State College, PA, USA
Biomonika (Noolean)3.0k wrote:

enter image description here

I want to visualise insert sizes in my mate-pair library and calculate statistics like mean, standard deviation..

I have found this tool 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!

statistics • 2.4k views
ADD COMMENTlink modified 3.3 years ago by madk00k320 • written 3.7 years ago by Biomonika (Noolean)3.0k
gravatar for Andre Elias
3.4 years ago by
Andre Elias80
Rio de Janeiro, Brazil
Andre Elias80 wrote:

Hi, it looks interesting, but I'm a bit confused. I did some googling and apparently it's a haskell program, so after digging around and installing haskell, it complains my samtools is not >0.2.1. I checked on the samtools official website and the most current version is 0.1.9. I looked online again and apparently there is a samtools 0.2.2 as a 'cabal' package, but it requires a few other dependencies…

Am I missing something? Is there any way that's a little more straightforward to install/compile Bamstats?

ADD COMMENTlink written 3.4 years ago by Andre Elias80

Did you figure out how to install this? Please let me know if you get this thing working.


ADD REPLYlink written 3.3 years ago by arnstrm1.6k
gravatar for madk00k
3.3 years ago by
madk00k320 wrote:

Try Qualimap. It computes mean, median and standard deviation of the insert size. Additionally it computes the histogram of insert sizes and plots insert size across reference.

ADD COMMENTlink written 3.3 years ago by madk00k320
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