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Hi,
I am using QuasR (great package!) to map genes to the C. elegans genome. The worm genome is smaller and the introns are a lot smaller than the mammalian ones. Is there a way to pass parameters to the mapper in qAlign to change the -max_intron and -min_intron parameters of Splicemap?
Thanks!
Peter
Hi Peter
Have you tried using the 'alignmentParameter' argument of qAlign? eg qAlign("samples.txt", "mygenome.fa", splicedAlignment=TRUE, alignmentParameter="max_intron = 100 min_intron = 10 ", clObj=foo)
But I am not sure if "alignmentParameter" is actually used when 'splicedAlignment=TRUE'.....
Michael Stadler is back on Monday and he will probaly have a better answer.
Regards, Hans-Rudolf