A comparison between whole transcript and 3’ RNA sequencing methods using Kapa and Lexogen library preparation methods

Table 1 The number of differentially expressed transcripts detected by the Trad-KAPA and 3’-LEXO, before and after subsampling from 10 million reads

Sequencing Depth	Trad-KAPA	Intersection (with 10 m)	3’-LEXO	Intersection (with 10 m)	Intersection (Trad-KAPA and 3’-LEXO)
1 million	343	339 (98.8%)	257	249 (96.9%)	177
2.5 million	758	742 (97.9%)	474	460 (97.0%)	329
5 million	1234	1194 (96.8%)	777	740 (95.2%)	562
10 million	1982	1982	1157	1157	882

The first column denotes the sequencing depth (i.e. the total number of mapped reads from the library examined). The second column denotes the number of differentially expressed transcripts detected by Trad-KAPA. The third column denotes the number of differentially expressed transcripts detected after subsampling that overlap with those from the 10 million sequencing depth. The fourth and fifth columns denote the results for the 3’-LEXO method. The sixth column denotes the number of differentially expressed transcripts detected by both the Trad-KAPA and the 3’-LEXO methods at listed sequencing depth

ISSN: 1471-2164