Changes between Version 92 and Version 93 of SOPs/atac_Seq

Timestamp:

08/19/21 17:03:45 (3 years ago)

Author:

thiruvil

Comment:

--

SOPs/atac_Seq

@@ -98 +98 @@
 === [=#call_peaks Call peaks] ===
 
-MACS v2 is applicable for ATAC-Seq using the appropriate options/parameters. 
+MACS v2 is applicable for ATAC-Seq using the appropriate options/parameters.
 
   * If you have human (hg38, hg19) and mouse (mm10, mm9) samples with biological replicates, you run [[https://github.com/ENCODE-DCC/atac-seq-pipeline|ENCODE ATAC-seq Pipeline]]. The pipeline takes fastq files, cleans and maps the reads, filters aligned reads and does peak calls. Here is the [[https://www.encodeproject.org/pipelines/ENCPL787FUN/|schema of the workflow]].  In addition, it does quality controls. Here is a [[http://barc.wi.mit.edu/education/hot_topics/ChIPseq_ATACseq_2021/qc.html | sample QC report]]. The steps below shows you how to run it on our Whitehead server. 
@@ -132 +132 @@
       * Before running ENCODE pipeline, verify there is no preexisting      conda startup code with the command below:
 {{{
-        conda env list
+conda env list
 }}}
        You have no preexisting conda if you get "conda: command not found". Otherwise, log out, log back in, start the new conda instance, and activate encode-atac-seq-pipeline