Changes between Version 102 and Version 103 of SOPs/atac_Seq

Timestamp:

01/12/23 11:49:37 (2 years ago)

Author:

gbell

Comment:

--

SOPs/atac_Seq

@@ -239 +239 @@
 
 }}}
-         Next, run mkarv on the JSON files to generate the interactive web viewer. By default, SRR891268 will be used as the reference sample in the viewer. You can specify a different reference when you built your viewer instance, refer to the information on how to configure the reference with mkarv -h.
+
+Next, run mkarv on the JSON files to generate the interactive web viewer. By default, SRR891268 will be used as the reference sample in the viewer. You can specify a different reference when you built your viewer instance, refer to the information on how to configure the reference with mkarv -h.
 
 {{{
@@ -255 +256 @@
    * 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
 {{{
-bedtools intersect -v -a ${PEAK} -b ${BLACKLIST} \
-                 | awk 'BEGIN{OFS="\t"} {if ($5>1000) $5=1000; print $0}' \
-                 | grep -P 'chr[\dXY]+[ \t]'  | gzip -nc > ${FILTERED_PEAK}
-
+bedtools intersect -v -a ${PEAK} -b ${BLACKLIST} | gzip -nc > ${FILTERED_PEAK}
 }}}