Question: RepeatMasker:understanding buildSummary.pl output
1
gravatar for freddiejung
3.3 years ago by
freddiejung20
Japan
freddiejung20 wrote:

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 does these values mean?

repeatmasker genome • 1.1k views
ADD COMMENTlink written 3.3 years ago by freddiejung20
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