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 | ||