. 2014 Jun 16;21(5):491–498. doi: 10.1093/dnares/dsu015

Table 1.

Summary of the MiSeq read data processing

Retrotransposon	Analysis	No. of read pairs	No. of collapsed reads (≥10)	Ratio (%)	No. of clusters
Rtsp-1	Raw data	3,567,587		100
	Validation of retrotransposon sequence	3,095,771	16,428	86.8
	Trimming to 50 bp	3,095,771	8,038	86.8
	QV filtering (≥20)	2,292,344	5,245	64.3
	Outlier filtering (>99%)	2,273,707	5,218	63.7
	Clustering with BLAT^a				1,497
LIb	Raw data	834,052		100
	Validation of retrotransposon sequence	743,945	3,608	89.2
	Poly(A) tail trimming (A ≥ 3)	743,935	3,571	89.2
	Trimming to 50 bp	743,935	3,154	89.2
	QV filtering (≥20)	434,502	1,619	52.1
	Outlier filtering (>98%)	427,120	1,603	51.2
	Clustering with BLAT^a				527

^aThe clusters include groups of two or more sequences and non-clustered single sequences for the insertion sites of Rtsp-1and LIb, where the minimum number of reads for an identical sequence was 10.