qingxiangguo / CCPRD-v.1.0

Pipeline for customized comprehensive proteomic reference database (CCPRD)
MIT License
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problem with merge_repeatMasker_out.pl output #1

Closed baishengjun closed 1 year ago

baishengjun commented 4 years ago

It is my genome.repeat.stats results:

total 169152450 bp sites were identified to be repeat

DNA:
        CMC-EnSpm       10728   11492609
        IS3EU   9       10560
        MULE-MuDR       1244    1140491
        PIF-Harbinger   8241    5407724
        PIF-Harbinger?  3068    1997085
        TcMar-Pogo      134     80102
        TcMar-Stowaway  91      15364
        hAT     40      8839
        hAT-Ac  5733    1925409
        hAT-Charlie     153     80293
        hAT-Tag1        6893    2722830
        hAT-Tip100      1538    828712
LINE:
        CR1     102     39022
        L1      3157    2955480
        L2      344     167142
        RTE-BovB        23      9131
LTR:
        Cassandra       605     67076
        Caulimovirus    1085    836015
        Copia   37787   22113715
        Copia?  21      34557
        ERVL    25      35625
        Gypsy   82762   56506518
RC:
        Helitron        46187   21723524
SINE:
        tRNA    14708   2141781
        tRNA-RTE        8       5168
Satellite:
        centr   1       195

DNA     5888    1789648
LTR     798     191481
Low_complexity  47533   2623677
SINE    471     78478
SINE?   554     89416
Satellite       1471    444027
Simple_repeat   187779  8468370
Unknown 107777  31027899
rRNA    183     232874
snRNA   57      10340
tRNA    557     79919

` 怎么解读这个输出结果,比如LTR有多少elements和长度是多少 还有像SINE和SINE?这种是什么意思?

Thanks in advance

qingxiangguo commented 1 year ago

Hi Sorry for the too late response.

The LINEs are longer non-LTR retrotransposons, while SINEs are much shorter non-LTR retrotransposons. This table shows the exact number of each type of repeats.

Hope you find this helpful.

Allen