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Table 1 Comparison of RNA-seq and transcript counting

From: High-throughput and quantitative genome-wide messenger RNA sequencing for molecular phenotyping

   lamc1 sa379 mdn1 sa1349
  Library protocol RNA-seq TC RNA-seq TC
  Number of libraries x6 x12 x6 x8
1 Number of read 2s mapped 146M 84M 119M 97M
2 Reads removed as duplicates 31.4 % 11.7 % 25.3 % 9.8 %
3 Counts (map to ENSG or called as peaks) 67M 52M 61M 61M
4 Number of counts matching MT transcripts 2.25M 5.51M 1.23M 3.73M
5 Proximity TC 3′ end and Ensembl transcript in bases NA −100 to 5000 −100 to +100 NA −100 to 5000 −100 to +100
6 Number of counts calling genes (no MT) 65M 21M 14M 60M 24M 19M
7 [Number of counts used to call transcripts] - 27M 16M - 31M 20M
8 Number of genes detected (no MT) 27732 14544 9906 28455 17138 11419
9 [Number of transcripts detected] - 21220 10574 - 25034 12144
10 Protein-coding genes with pval obtained 24256 13763 9542 25012 16220 10967
11 Protein-coding genes with adj pval obtained 15883 12139 8555 22034 14886 10184
12 And with an adj pval <=0.05 1468 227 162 9529 2649 2013
13 And fold change >=2 235 141 103 2255 1534 1121
14 Genes identified by RNA-seq and TC       
15 Genes from row 10 identified by both 11114 11114   14791 14791  
16 And with an adj pval <=0.05 and FC >2 131 126   1443 1427