# Sequencing depth and read length considerations for TruSeq Stranded RNA libraries

**What is the recommended run length and type for these libraries?**\
The read length and format (single read versus paired end) are important considerations in the design of RNA sequencing experiments. The table below provides general guidance on some factors to consider - note that these are common configurations and read lengths, but not official recommendations. Needs for individual projects may vary based on multiple variables as well as user preference. M = million.

|                                                        |                  |                                        |
| ------------------------------------------------------ | ---------------- | -------------------------------------- |
| Applications                                           | Read Type        | Read depth / sample (mRNA / total RNA) |
| Gene profiling (gene-level counts)                     | 1 x 50           | >5M / >10M                             |
| Discovery (alternative transcripts, gene fusions, etc) | 2 x 50 - 2 x 75  | ≥50M / >100M                           |
| Complete transcripome annotation                       | 2 x 75 - 2 x 100 | ≥100M / ≥200M                          |

**Why does Illumina recommend paired-end sequencing of stranded RNA libraries?**\
Due to the directional nature of the assay, paired-end sequencing captures both ends of the RNA molecule, and allows for assessing true duplicate rates.

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