Changes between Version 26 and Version 27 of SOPs/atac_Seq
- Timestamp:
- 10/06/20 13:15:12 (4 years ago)
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TabularUnified SOPs/atac_Seq
v26 v27 49 49 }}} 50 50 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 deepTools package: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 deepTools package: 52 52 {{{ 53 53 alignmentSieve -b foo.bam --blackListFileName hg38-blacklist.bed -o no_blackList.bam
