Entering edit mode
5.3 years ago
wambuimbichi
•
0
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
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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 %)
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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)
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.Thank you!