| 51 | | * For samples from human/mouse/fly/c.elegans, remove reads mapped to the ENCODE blacklist. Blacklist is a a comprehensive set of genomic regions that have anomalous, unstructured, or high signal in next-generation sequencing experiments independent of cell line or experiment. [https://www.nature.com/articles/s41598-019-45839-z | ENCODE paper ]. The blacklist can be downloaded from [https://github.com/Boyle-Lab/Blacklist/]. |
| | 51 | * For samples from human/mouse/fly/c.elegans, remove reads mapped to the ENCODE blacklist. Blacklist is a a comprehensive set of genomic regions that have anomalous, unstructured, or high signal in next-generation sequencing experiments independent of cell line or experiment. [https://www.nature.com/articles/s41598-019-45839-z | ENCODE paper ]. The blacklist can be downloaded from [https://github.com/Boyle-Lab/Blacklist/]. Blacklist can be filtered with alignmentSieve from deeptool package: |
| | 52 | {{{ |
| | 53 | alignmentSieve -b foo.bam --blackListFileName hg38-blacklist.bed -o no_blackList.bam |
| | 54 | }}} |
