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Old 05-12-2016, 04:26 AM   #302
Simon Andrews
Location: Babraham Inst, Cambridge, UK

Join Date: May 2009
Posts: 871

There's no built in support for this kind of customisation, but you could build this yourself if you like.

If you have a look in the automated genome you will quickly see how to play around with the way the pseudo chromosomes are made. There are two files which matter here:

chr_list is a text file giving the names and total lengths of the genomes. In a normal build only the pseudo chromosomes would appear in here, but you could add in some individual scaffolds on their own if you like.

aliases.txt is the file which says how the individual sequence files you have map into the chromosomes (or pseudo chromosomes in this case). For each sequence it says which chromsome it maps to and where in that chromosome it starts. If the number is negative then the sequence is assumed to be reverse complemented and inserted at that position.

By editing these two files manually you should be able to group your sequences however you like in the newly built genome.

Let me know how you get on.
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