Changes between Version 23 and Version 24 of SOPs/atac_Seq

Timestamp:

10/06/20 13:01:16 (4 years ago)

Author:

byuan

Comment:

--

SOPs/atac_Seq

@@ -48 +48 @@
 samtools view -h file.bam | grep -v chrM | samtools view -b -h -f 0x2 - | samtools sort - > file.sorted.bam
 }}}
+
+   * 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/]. 
+
 
 === [=#QC Run quality control and calculate QC metrics] ===