I'm working with an unassembled genome of cephalopod and I would to find transposable elements. My idea is to use repeatscout to generate a library and repeatmasker to find the elements. After creating a library with repeatscout, I run Repeatmasker but it generates a table like this:
file name: OB_100DEC.fa
sequences: 100
total length: 209466439 bp (184235452 bp excl N/X-runs)
GC level: 35.24 %
bases masked: 73100024 bp ( 34.90 %)
==================================================
number of length percentage
elements* occupied of sequence
--------------------------------------------------
SINEs: 0 0 bp 0.00 %
ALUs 0 0 bp 0.00 %
MIRs 0 0 bp 0.00 %
LINEs: 0 0 bp 0.00 %
LINE1 0 0 bp 0.00 %
LINE2 0 0 bp 0.00 %
L3/CR1 0 0 bp 0.00 %
LTR elements: 0 0 bp 0.00 %
ERVL 0 0 bp 0.00 %
ERVL-MaLRs 0 0 bp 0.00 %
ERV_classI 0 0 bp 0.00 %
ERV_classII 0 0 bp 0.00 %
DNA elements: 0 0 bp 0.00 %
hAT-Charlie 0 0 bp 0.00 %
TcMar-Tigger 0 0 bp 0.00 %
Unclassified: 560941 66374119 bp 31.69 %
Total interspersed repeats: 66374119 bp 31.69 %
Small RNA: 0 0 bp 0.00 %
Satellites: 0 0 bp 0.00 %
Simple repeats: 290711 15358198 bp 7.33 %
Low complexity: 0 0 bp 0.00 %
==================================================
* most repeats fragmented by insertions or deletions
have been counted as one element
The query species was assumed to be homo
RepeatMasker Combined Database: Dfam_Consensus-20181026
run with rmblastn version 2.6.0+
The query was compared to unclassified sequences in ".../OB_100DEC_repeats_filtered1.fa"
This was my command to run repeatmasker:
./RepeatMasker -s -lib /home/RepeatScout-1.0.5/OB_100DEC_repeats_filtered1.fa /home/Workdirectory/OB_100DEC.fa
The file OB_100DEC_repeats_filtered1.fa
is the output of repeatscout and looks like this:
>R=3 (RR=4. TRF=0.000 NSEG=0.000)
TAAGGCGGCGAGCTGGCAGAATCGTTAGCACGCCGGGCGAAATGCTTAGCGGTATTTCGTCTGTCTTTACGTTCTGAGTT
CAAATTCCGCCGAGGTCGACTTTGCCTTTCATCCTTTCGGGGTCGATAAAATAAGTACCAGTTGAGCACTGGGGTCGATG
TAATCGACTTACCCCCTCCCCCAAAATTTCTGGCCTTGTGCCTATATTAGAAACGATTATT
>R=4 (RR=5. TRF=0.122 NSEG=0.226)
ACACACACACACACACACACACACACATATATATATATATACATATATACGACGGGCTTCTTTCAGTTTCCGTCTACCAA
ATCCACTCACAAGGCTTTGGTCGGCCCGAGGCTATAGTAGAAGACACTTGCCCAAGGTGCCACGCAGTGGGACTGAACCC
GGAACCATGTGGTTGGTAAGCAAGCTACTTACCACACAGCCACTCCTGCGCCTATATATAT
>R=6 (RR=7. TRF=0.134 NSEG=0.247)
TTGTTTCAGTCATTTGACTGCGGCCATGCTGGAGCACCGCCTTTAGTCGAGCAAATCGACCCCAGGACTTATTCTTTGTA
AGCCTAGTACTTATTCTATCGGTCTCTTTTGCCGAACCGCTAAGTTACGGGGACGTAAACACACCAGCATCGGTTGTCAA
GCGATGTTGGGGGGACAAACACAGACACACAAACACACACACACACATACATATATATATATATATATATA
>R=8 (RR=9. TRF=0.391 NSEG=0.000)`
and it is composed by all the TE (not classified) find in all the scaffolds of the genome.
Can anyone explain why there are no TE? The fasta file that I used is only a part of the whole genome, it is about 200 mb and it is composed by the 100 greatest scaffolds of my genome. Maybe I made a mistake with the use of libraries. Anyway I installed RepeatMasker with rmblastn version 2.6.0+ and RepeatMasker Combined Database: Dfam_Consensus-20181026. thank you
OB_100DEC_repeats_filtered1.fa
? $\endgroup$