Changes between Version 25 and Version 26 of SOPs/atac_Seq


Ignore:
Timestamp:
10/06/20 13:12:46 (4 years ago)
Author:
byuan
Comment:

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  • SOPs/atac_Seq

    v25 v26  
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    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:
     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:
    5252{{{
    5353alignmentSieve -b foo.bam --blackListFileName hg38-blacklist.bed -o no_blackList.bam