| Software | Version | |
|---|---|---|
| RNA-seq | hisat2 | 2.0.5 |
| samtools | 0.1.18 | |
| stringtie | v1.3.6 | |
| WGBS_RRBS | Bismark | v0.22.3 |
| bowtie2 | 2.1.0 | |
| ATAC-seq | bowtie2 | 2.3.5.1 |
| samtools | 0.1.18 | |
| macs2 | 2.2.6 | |
| picard | 2.25.5 | |
| bedtools | 2.29.2 | |
| ChIP-seq | bowtie2 | 2.3.5.1 |
| samtools | 0.1.18 | |
| macs2 | 2.2.6 | |
| MeRIP-seq | bowtie2 | 2.3.5.1 |
| samtools | 0.1.18 | |
| macs2 | 2.2.6 | |
| miRNA-seq | miRDeep2 | 0.1.3 |
| miRanda | 1.2 |
