RepeatMasker Analysis Pipeline
Authors: Andrew Shedlock, Quan Fang, Chris Botka, Amir Karger, Greg Cavanagh
Affiliation:
College of Charleston, Department of Biology Hollings Science Center 58 Coming Street, Room 216B Charleston, SC 29401 USA
Research Computing, Harvard Medical School 107 Avenue Louis Pasteur, Room 105, Boston MA 02115-5701
Contact: botka@hms.harvard.edu, shedlockam@cofc.edu, fangquans@gmail.com
RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. We developed RMPipeline, as a secondary level repeats analysis pipeline.
(1) concatenates repeatmasker .out resutls into a master file, named MasterFile.out
(2) categorize repeats into families, superfamilies and subfamilies.
usage:
user@orchestra$ perl family_cli.pl -r RepeatMasker -f RMFamily -S RMSuper -s RMSub
RepeatMasker = RepeatMasker raw outputs directory
RMFamily = Directory to place repeat families
RMSuper = Directory to place repeat super families
RMSub = Directory to place repeat sub families
logfile:
RepeatMasker raw results directory: RepeatMasker_orchestra/
MasterFile.out done
Your source MasterFile.out file
Output folder: RMFamily/
RMFamily done
Your source RepeatMaskerFamily directory: RMFamily/
Your output RepeatMaskerSuperFamily directory: RMSuper
RMSuperFamily done
Your source RepeatMaskerFamily directory: RMFamily/
Your output RepeatMaskerSubFamily directory: RMSub
RMSubFamily done
Extracts all the repeats sequence from original supercontigs. Mainly for GC contents. The design diagram is attached as GC_cli.pdf
usage:
user@orchestra$ perl GC_cli.pl -M Masterfile -F Superfasta -f FamilyCategory -O Output
Masterfile = Masterfile of the species, under RM raw directory
Superfasta = Source genome data, in fasta Format
FamilyCategory = [Optional] Editable family categorization file, based on user's knowledge
Output = [Optional] Output directory
FamilyCategory.txt is strictly a tab delimited file, "family super-family sub-family", for example:
DNA DNA ELEMENTS D-OTHER
DNA DNA ELEMENTS D-OTHER
DNA_Academ DNA ELEMENTS D-OTHER
DNA_Chapaev DNA ELEMENTS D-OTHER
Summarize RepeatMasker raw data, concatenates into a MasterFile.tbl. The design diagram is attached as tbl.pdf
usage:
user@orchestra$ perl tbl.pl -r RepeatMasker
RepeatMasker = RepeatMasker raw outputs directory
MasterFile.tbl will be created under the RepeatMasker directory
MasterFile.tbl:
sequences: 393681
total length: 2187967980 bp (1941067579 bp excl N/X-runs)
GC level: 43.6973309922616 %
bases masked: 131962953 bp ( 6.0313018383386 %)
==================================================================
(1)number of element (2)length occupied (3)percentage of sequence
------------------------------------------------------------------
Retroelements 420205 111474566 bp 5.0949 %
SINEs: 92706 10798749 bp 0.4936 %
Penelope 381 30186 bp 0.0014 %
LINEs: 300463 94280632 bp 4.3090 %
CRE/SLACS 0 0 bp 0.0000 %
L2/CR1/Rex 275225 86629285 bp 3.9593 %
R1/LOA/Jockey 2359 928603 bp 0.0424 %
R2/R4/NeSL 80 9535 bp 0.0004 %
RTE/Bov-B 15922 5300324 bp 0.2422 %
L1/CIN4 5651 1213003 bp 0.0554 %
LTR elements: 27036 6395185 bp 0.2923 %
BEL/Pao 520 27999 bp 0.0013 %
Ty1/Copia 65 4575 bp 0.0002 %
Gypsy/DIRS1 12673 5240062 bp 0.2395 %
Retroviral 11009 853484 bp 0.0390 %
DNA transposons 83672 7572146 bp 0.3461 %
hobo-Activator 42532 2858794 bp 0.1307 %
Tc1-IS630-Pogo 15192 1735841 bp 0.0793 %
En-Spm 2 153 bp 0.0000 %
MuDR-IS905 0 0 bp 0.0000 %
PiggyBac 4412 724574 bp 0.0331 %
Tourist/Harbinger 362 30309 bp 0.0014 %
Other (Mirage, 30 1907 bp 0.0001 %
Rolling-circles 0 0 bp 0.0000 %
Unclassified: 9471 1465230 bp 0.0670 %
Total interspersedrepeats: 120511942 bp 5.5079 %
Small RNA: 20136 2745203 bp 0.1255 %
Satellites: 2069 166911 bp 0.0076 %
Simple repeats: 115056 4668582 bp 0.2134 %
Low complexity: 200688 6490805 bp 0.2967 %
Poster: Quan Fang, Christopher Botka and Andrew Shedlock. Global annotation and molecular evolutionary analysis of genomic repeats in the Painted Turtle, Chrysemys picta. 3rd International Conference/Workshop on Genomic Impact of Eukaryotic Transposable Elements.