Struc_hg19: MEA RNA 2ndary structures of hg19 exons predicted by RNAfold

In ZhenWei10/m6ALogisticModel: Linear model analysis on RNA modification data.

Description

The full length transcripts are extracted from hg19; the transcript annotation file was downloaded from the refSeq archive-2015-07-17-14-32-32. The temperature of RNAfold prediction was set at 70 degree, and the gammar for MEA structure was set at 0.1. The maximum paring distance was set at 150bp.

Usage

rBS_gr = GRanges(seqnames = rBS_df$`#SeqID`, strand = rBS_df$refStrand, ranges = IRanges(start = rBS_df$refPos, width = 1))
rBS_gr_filtered <- rBS_gr[!rBS_gr %over% Struc_hg19]

Format

A GRangesList object of length 53350:

Each element of the GRangesList represents a transcript, exept that the first element refers to the mitochondria chromosome. The GRanges within each of the GRangesList element represent the genomic locations of the MEA RNA 2ndary structures predicted by the method above.

Details

For the transcripts longer than 8000bp, the predictions were conducted in windows of 2000bp with steps of 1000bp.

ZhenWei10/m6ALogisticModel documentation built on May 17, 2019, 10:11 p.m.