Extract Synteny Blocks from 46 way multiz alignment maf file

[Meenakshi Bagadia]

Hi Everyone,

I am trying to use Maffilter to extract the synteny blocks from 46 way multiz alignment maf files.
For example for 10 organisms (dog, human, rabbit, hedgehog, tenrec, etc), I need synteny regions ( chromosome/scaffold positions )in each organism.

 
I tried the Merge option. But I am not sure how to optimized the parameters i.e. max_dist in order to capture the largest syntenic blocks.

Other question is how to get the desired output (specifically coordinate positions for all organisms ).
I used Output : it is again a MAF file, which is not easy to grasp.
I tried OutputAlignments : it is giving me only the reference genome block coordinates, not the rest genomes.

Is there any script or  any other approach from which I can get the results in much more readable and easy format to handle.

Thanks in advance

Meenakshi

[Julien Yann Dutheil]

Deae Meenakshi,

There is no absolute rule for max_dist, you have to play around with its value and see what gives the best output for your needs. Longer distance make larger blocks, but introduces missing data.

In order to get coordinates, see http://biopp.univ-montp2.fr/manual/html/maffilter/v1.1.0/OutputCoordinates.html#OutputCoordinates

J.