I used VEP and REP to remove vector and ALU repeat sequences
from the sequence text files. I would like to clarify a few points.
Does VEP remove vector sequence for you? It seems to create a file
with extension corresponding to vector name and the original file
have nothing in it. How can one remove partial vector sequence?
REP creates a filename with extension .ALU, when I look at the
contents of that file I found it to be the same as the original
except for a head indicating a number e.g. 5 100. Does this mean that
sequence 5 to 100 is ALU and should be ignored? Is there anyway using
Staden software, that I can remove ALU sequences from text files
automatically? If so how?
rifat at icr.ac.uk