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Figure 1 | BMC Genomics

Figure 1

From: Beyond cleaved small RNA targets: unraveling the complexity of plant RNA degradome data

Figure 1

Analysis schemas for motifs associated with uncapped 5′-ends. The analysis pipeline for identifying motifs associated with uncapped 5′-ends (A). Uncapped 5′-ends were first classified by the genomic region where they were produced by mapping with Bowtie. Selected uncapped 5′-ends representing as major peaks were further filtered with the binomial test. After filtering known miRNA targets, all the uncapped 5′-ends which passed the threshold of the binomial test or the top 1000 most abundant ends in each genomic region were subjected to motif analysis with the MEME suite. The spatial relationship between motifs and uncapped reads on a genome-wide scale was further explored by MORPH (B). All loci containing a candidate motif in a specific genomic region were first identified and then clustered based on the distribution of normalized reads in a 20-nt region flanking the motif. With the first nucleotide of the motif set as 1, positions upstream of the motif are indicated as negative values and positions downstream are indicated as positive values. The position of an uncapped read was determined by its 5′-end and the number of uncapped reads at each position was normalized to the total read number within the 20-nt region and represented as a heat map.

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