Arbidopsis_smallRNA_loci
Publication
Thomas J. Hardcastle, Sebastian Y. Müller & David C. Baulcombe Scientific Reports volume 8, Article number: 6338 (2018) https://www.nature.com/articles/s41598-018-24515-8
Public data
https://www.ebi.ac.uk/ena/data/view/PRJEB22276
Additional material for small RNA loci project
GFF file contains all annotation used to class sRNA-loci in Arabidopsis. The 9 cluster described in the paper are saved as cluster. See below an example R snippet to access:
library(rtracklayer)
loci <- import.gff3(file.path("lociV_gr9.gff3"))
length(loci)
# [1] 24559
head(loci[,c("ID", "cluster")])
# GRanges object with 6 ranges and 2 metadata columns:
# seqnames ranges strand | ID cluster
# <Rle> <IRanges> <Rle> | <character> <character>
# [1] 1 [ 690, 1022] * | ATSL000010 5
# [2] 1 [ 1023, 1070] * | ATSL000020 4
# [3] 1 [ 8629, 8700] * | ATSL000040 3
# [4] 1 [11911, 11933] * | ATSL000050 1
# [5] 1 [13006, 13043] * | ATSL000060 1
# [6] 1 [16957, 17154] * | ATSL000070 7
# -------
# seqinfo: 5 sequences from an unspecified genome; no seqlengths
table(loci$cluster)
#
# 1 2 3 4 5 6 7 8 9
# 5242 2808 2196 1788 4787 2898 2240 1259 1341