| 188 | | ==== Other Tools ==== |
| 189 | | |
| 190 | | [[https://github.com/LiuLabUB/HMMRATAC | HMMRATAC]] is another piece of software for ATAC-seq peak-calling. |
| | 188 | ==== Other Tools or Options ==== |
| | 189 | |
| | 190 | * [[https://github.com/LiuLabUB/HMMRATAC | HMMRATAC]] |
| | 191 | * [[https://github.com/jsh58/Genrich | Genrich]] |
| | 192 | * Run MACS2 with BAMPE option for PE reads, i.e. -f BAMPE, this asks MACS pileup and infer the real fragment size from the alignment. Note: this option can be used to find accessible regions but not suitable for finding exact cut sites. Also, comparing this option with converting to BED format (above), the BAMPE peaks calls are more conservative and may miss real peaks. |
| | 193 | |
| | 194 | |
