TE.zip

Repetitive elements predicted by RepeatMasker (version 4.1.7-p1) for 25 grassland plant species.

Species list:
Species_code Species_name
GerPra Geranium pratense
LeuVul Leucanthemum vulgare agg.
TriFla Trisetum flavescens
LotCor Lotus corniculatus
CreBie Crepis biennis
BelPer Bellis perennis
DauCar Daucus carota
PruVul Prunella vulgaris
TriPra Trifolium pratense
PriVer Primula veris
HolLan Holcus lanatus
AloPra Alopecurus pratensis
GalMol Galium mollugo agg.
KnaArv Knautia arvensis
MedVar Medicago x varia
PlaLan Plantago lanceolata
LuzCam Luzula campestris
VerCha Veronica chamaedrys
ArrEla Arrhenatherum elatius
TriDub Trifolium dubium
LatPra Lathyrus pratensis
VicCra Vicia cracca
RanAcr Ranunculus acris
PlaMed Plantago media
AjuRep Ajuga reptans

Analyse pseudo code:
for i in {01..25}; do
# the number corresponding to a particular species
outputDir="BMK230426-BJ202-01P000${i}"
isoform="path/to/isoSeqData/BMK230426-BJ202-01P000${i}"
path/to/RepeatMasker -pa 16 -lib Viridiplantae.fa -dir $outputDir $isoform
done;