Iam working on transcriptome data from illumina genome analyzer II.I woudl like to do a velvet assembly for these short reads ,but i see lot of repeats and homopolymers like AAAAAAAAA and TTTTTTTTTTTTTTT, so i would like to know whether i should mask all the repeats before i start denovo assembly by using velvet.
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Hi ..
I am copying a reply from the velvet mailing list which I feel fits in here.
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If the absolute error length (as in the length difference between the
actual polymer and the one measured) is longer than 3bp and this error
has been observed more times than than the chosen coverage cutoff then
the error is maintained open. This is a lot of if's, so hopefully does
not occur too often.
The reason for this conservative stance on the error length is to avoid
drastic merging of genuine homopolymers (which are quite frequent). I
have not found any method to relax this constraint without having all
sorts of repeats collapse into each other.
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Best,
-Abhi
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