Question: Repeat Masker libraries
0
gravatar for wambuimbichi
5 weeks ago by
wambuimbichi0 wrote:

I am new to bioinformatics and have installed RepeatMasker successfully however one of my libraries RepeatMaskerLib.embl is incomplete and so when i mask a genome it only masks simple repeats and low complexity repeats. Someone please advise on how to fix this. Thanks

cat Ath.fa.tbl
==================================================
file name: Ath.fa                   
sequences:             7
total length:  119667750 bp  (119482146 bp excl N/X-runs)
GC level:         36.06 %
bases masked:    2211370 bp ( 1.85 %)
==================================================
               number of      length   percentage
               elements*    occupied  of sequence
--------------------------------------------------
Retroelements            0            0 bp    0.00 %
   SINEs:                0            0 bp    0.00 %
   Penelope              0            0 bp    0.00 %
   LINEs:                0            0 bp    0.00 %
    CRE/SLACS            0            0 bp    0.00 %
     L2/CR1/Rex          0            0 bp    0.00 %
     R1/LOA/Jockey       0            0 bp    0.00 %
     R2/R4/NeSL          0            0 bp    0.00 %
     RTE/Bov-B           0            0 bp    0.00 %
     L1/CIN4             0            0 bp    0.00 %
   LTR elements:         0            0 bp    0.00 %
     BEL/Pao             0            0 bp    0.00 %
     Ty1/Copia           0            0 bp    0.00 %
     Gypsy/DIRS1         0            0 bp    0.00 %
       Retroviral        0            0 bp    0.00 %

DNA transposons          0            0 bp    0.00 %
   hobo-Activator        0            0 bp    0.00 %
   Tc1-IS630-Pogo        0            0 bp    0.00 %
   En-Spm                0            0 bp    0.00 %
   MuDR-IS905            0            0 bp    0.00 %
   PiggyBac              0            0 bp    0.00 %
   Tourist/Harbinger     0            0 bp    0.00 %
   Other (Mirage,        0            0 bp    0.00 %
    P-element, Transib)

Rolling-circles          0            0 bp    0.00 %

Unclassified:            0            0 bp    0.00 %

Total interspersed repeats:           0 bp    0.00 %


Small RNA:               0            0 bp    0.00 %

Satellites:              0            0 bp    0.00 %
Simple repeats:      40167      1627651 bp    1.36 %
Low complexity:      10698       585594 bp    0.49 %
==================================================

* most repeats fragmented by insertions or deletions
  have been counted as one element


The query species was assumed to be arabidopsis   
RepeatMasker version development-$Id: RepeatMasker,v 1.332 2017/04/17 19:01:11 rhu
run with nhmmscan version 3.2.1 (June 2018)
software error • 93 views
ADD COMMENTlink modified 5 weeks ago by finswimmer8.9k • written 5 weeks ago by wambuimbichi0

Hello and welcome to biostars wambuimbichi ,

Please use the formatting bar (especially the code option) to present your post better. I've done it for you this time.
code_formatting

Thank you!

ADD REPLYlink written 5 weeks ago by finswimmer8.9k
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