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Fig. 1 | BMC Genomics

Fig. 1

From: Expression dynamics and relations with nearby genes of rat transposable elements across 11 organs, 4 developmental stages and both sexes

Fig. 1

Procedure to calculate differently expressed TEs and determine the relations between genes and TEs. a Mapping pipeline. Trimmomatic was used to trim data, and then BWA v0.7.12 with default parameters was used to mapping reads to genome. The iteres was used to calculate RPKM of all TE subfamilies in all samples. The cufflinks was used to calculate RPKM of each TE in all sample. The expression value of genes was downloaded from Rat BodyMap database. b Fold change and Bonferroni-corrected p-value were used to evaluate DETEs. c We calculated PCC and distance between TE and its nearest gene, and then explored relation between PCC and distance

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