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I'm currently analyzing some mutation data, I've used the pregap4 modules to set up my configurations. I've written a perl script (just need to lern TLC to actually change the modules ) looping aross the pregap function since I need to change reference trace for each individual and primer set.
In my experiment file the link to the reference trace is correct, however within the gap4 module when I choose the option to show the trace difference the reference trace and tumor trace does not sync I have maybe 50 reads in each Contig and they are totally scrambled when it comes to visually inspect the traces.
This is actually the main reason why I choose staden to quickly be able to validate the annotated Indels and SNPs incorporated from other calling modules such as CHILD and polyphred. Have anyone else had this problem before?.
Thanks in advance! (I want to be able to use the software since it was such a pain to build on my max os x system :) ).