Changes between Version 27 and Version 28 of SOPs/atac_Seq

Timestamp:

10/08/20 11:14:59 (5 years ago)

Author:

gbell

Comment:

--

SOPs/atac_Seq

@@ -49 +49 @@
 }}}
 
-   * 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:
-{{{
-alignmentSieve -b foo.bam --blackListFileName hg38-blacklist.bed -o no_blackList.bam
+   * For samples from human, mouse, fly, or C. elegans, one can prevent some probable false-positive peaks by removing reads that overlap "blacklisted" regions.  The blacklist, [https://www.nature.com/articles/s41598-019-45839-z popularized by ENCODE], 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. The blacklist regions can be downloaded from [https://github.com/Boyle-Lab/Blacklist/].  We have them on Whitehead servers at /nfs/BaRC_datasets/ENCODE_blacklist/Blacklist/lists
+
+   * Reads overlapping the blacklist can be filtered using alignmentSieve (from the deepTools package) or 'intersectBed -v' (from the bedtools suite):
+{{{
+alignmentSieve -b Reads.bam --blackListFileName hg38-blacklist.bed -o Reads.no_blackList.bam
+intersectBed -v -a Reads.bam -b hg38-blacklist.bed > Reads.no_blackList.bam
 }}} 
+
+   * An alternative for handling blacklist regions is to keep the mapped reads as is but (further downstream) remove peaks overlapping blacklist regions.  Between-sample normalization will typically differ whether one filters these regions in reads or in peaks.
 
 
@@ -135 +140 @@
 {{{
 # add homer bin folder to your path, so the scripts called by findMotifsGenome.pl could be identified
-PATH=/YourPath/homer/v4.11(version)/bin/:$PATH
+PATH=/nfs/BaRC_Public/homer/bin:$PATH
 
 findMotifsGenome.pl peak.bed hg38 out_dir -size 300 -S 2 -p 5 -cache 100 -fdr 5 -mask -mknown Jaspar_hs_core_homer.motifs -mcheck Jaspar_hs_core_homer.motifs