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. Author manuscript; available in PMC: 2015 Oct 1.
Published in final edited form as: Methods. 2014 Jun 27;69(3):274–281. doi: 10.1016/j.ymeth.2014.06.008

Table 2.

Tools Used for MeRIP-Seq Differential RNA Methylation Analysis

Step Purpose Tools Flowchart
1 Raw data preprocessing and sequence alignment SRAtoolkit / Tophat [27] graphic file with name nihms-613746-t0004.jpg
2 RNA methylation sites identification and differential analysis exomePeak1 [12]
3 Motif identification Bedtools [28] / DREME [29]
4 Methylation sites visualization Samtools [30] / IGV [31]
5 Function analysis DAVID [24]
1

The exomePeak package was initially developed as a MATLAB package [12] for RNA methylation site detection from MeRIP-Seq data. It has been recently extended with differential analysis capacity and implemented as an open source R/Bioconductor package.