Hello, Apologies for the delay in replying. One of our developers had this to say about your question:
For human, we have a track Interrupted Rpts (Fragments of Interrupted Repeats Joined by RepeatMasker ID) that should provide what you are looking for. Unfortunately we don't have that track for dog. The ID column of RepeatMasker output used to contain a one-letter code, and was changed to contain the numeric ID but we decided that the value of the numeric ID was not enough to re-engineer the sql table and track code. Even if the rmsk table did contain the full numeric IDs, they would not be much use by themselves. The numeric IDs are not stable -- they are sequential IDs generated in each run of RepeatMasker. So they would not correspond between human and dog. In fact, since we run RepeatMasker as a cluster job on many fragments of the genome, the numeric IDs are not unique within the human Interrupted Rpts track; joining by numeric ID is done at the fragment-level after running RepeatMasker. Best regards, Pauline Fujita UCSC Genome Bioinformatics Group http://genome.ucsc.edu On 05/03/11 23:29, sydghyyh14 wrote: > I want to determine which repetitive fragments come from the same > transposable element. > At first, I downloaded the table of rmsk. But it told me that "First digit of > id field in RepeatMasker .out file. Best ignored" in the id field. > And then I downloaded the result of RepeatMasker from the directory of > bigZips. > But I found same fragment have the same ID, while they do not come from the > same transposable elememt. > Such as: canFam2 chromOut.tar.gz chr1 and ID 1 > hg18 chromOut.tar.gz chr1 and ID1 > Who can tell me how to determine which fragments come from the same > transposable element ? > > > > > 2011-05-04 > > > sydghyyh14 > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
