Entering edit mode
5 months ago
sansan96
▴
140
Hello everyone,
I just ran RepeatModeler and RepeatMasker to identify repeats in a fungal genome and mask them but I see that the RepeatMasker output doesn't look like I expected. I see that there are no elements corresponding to DNA transposons, satellites and SINEs. Am I doing something wrong? In other species of the same fungal, elements that are not shown in my fungal are present.
The script I executed was the following:
# Run RepeatModeler
BuildDatabase -name fungal_T9 fungal_T9_kmer.fasta
RepeatModeler -database fungal_T9 -threads 8 -LTRStruct
# Run RepeatMasker
RepeatMasker fungal_T9_kmer.fasta -lib consensi.fa.classified -xsmall -gff -pa 8 -s -dir RepeatMasker_consensi/
The output of RepeatMasker::
fungal_T9_kmer.fasta.cat.gz
fungal_T9_kmer.fasta.out
fungal_T9_kmer.fasta.tbl
fungal_T9_kmer.fasta.masked
fungal_T9_kmer.fasta.out.gff
My fungal_T9_kmer.fasta.tbl file:
==================================================
file name: fungal_T9_kmer.fasta
sequences: 142
total length: 39853892 bp (39853892 bp excl N/X-runs)
GC level: 48.24 %
bases masked: 2066966 bp ( 5.19 %)
==================================================
number of length percentage
elements* occupied of sequence
--------------------------------------------------
Retroelements 530 1139611 bp 2.86 %
SINEs: 0 0 bp 0.00 %
Penelope: 0 0 bp 0.00 %
LINEs: 92 180401 bp 0.45 %
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: 438 959210 bp 2.41 %
BEL/Pao 0 0 bp 0.00 %
Ty1/Copia 0 0 bp 0.00 %
Gypsy/DIRS1 342 812490 bp 2.04 %
Retroviral 96 146720 bp 0.37 %
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 %
MULE-MuDR 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: 1549 496138 bp 1.24 %
Total interspersed repeats: 1635749 bp 4.10 %
Small RNA: 0 0 bp 0.00 %
Satellites: 0 0 bp 0.00 %
Simple repeats: 8560 360341 bp 0.90 %
Low complexity: 1434 70876 bp 0.18 %
==================================================
* most repeats fragmented by insertions or deletions
have been counted as one element
RepeatMasker version 4.1.5 , sensitive mode
run with rmblastn version 2.14.1+
The query was compared to classified sequences in ".../consensi.fa.classified"
FamDB:
