Entering edit mode
8.4 years ago
freddiejung
▴
60
Dear all,
I have a question about buildSummary.pl output file.
I masked the repetitive sequences of my species with RepeatMasker and then,
to summarize the ".out" file, run the buildSummary.pl.
The output was like this:
Class Count bpMasked %masked
===== ===== ======== =======
DNA 1969 223547 0.05%
Academ 142 33614 0.01%
CMC-Chapaev-3 1260 342592 0.08%
Crypton 602 153846 0.03%
Ginger 5938 391178 0.09%
Kolobok-Hydra 315 97205 0.02%
PiggyBac 185 102838 0.02%
Sola 1175 268275 0.06%
TcMar 280 55229 0.01%
TcMar-Mariner 8418 1800910 0.40%
TcMar-Pogo 494 85211 0.02%
TcMar-Tc1 2449 774137 0.17%
TcMar-Tigger 7605 1500599 0.33%
TcMar-m44 237 63503 0.01%
Zator 16572 2514982 0.56%
hAT-Ac 2757 456475 0.10%
hAT-Blackjack 398 67475 0.02%
hAT-Charlie 6415 1594868 0.36%
hAT-Tip100 736 158205 0.04%
LINE 1315 369211 0.08%
CR1 11117 3176498 0.71%
CR1-Zenon 8308 1872769 0.42%
CRE-II 2453 627549 0.14%
Dong-R4 95 16167 0.00%
I 3763 1430329 0.32%
I-Nimb 756 142298 0.03%
Jockey 53071 12137357 2.71%
L1 6810 627076 0.14%
L1-Tx1 404 70964 0.02%
L2 36183 9967678 2.22%
LOA 5842 2460653 0.55%
Penelope 3556 621028 0.14%
Proto2 432 151578 0.03%
R1 37655 7955606 1.77%
R2-Hero 280 70696 0.02%
RTE-BovB 34559 8702656 1.94%
RTE-RTE 31059 5364423 1.20%
..........
I found "Count", " bpMasked" and "%masked" of the rows of "DNA" and "LINE" are filled with certain values. These values are clearly not the summary of the transposonal class.
In my case, there are "--" in "Count", " bpMasked" and "%masked" at the rows of "SINE" or "LTR".
What is the difference between "DNA"/"LINE" and "SINE"/"LTR"?
What do these values mean?
