Changes between Version 68 and Version 69 of SOPs/atac_Seq

Timestamp:

07/07/21 18:48:23 (4 years ago)

Author:

byuan

Comment:

--

SOPs/atac_Seq

@@ -64 +64 @@
 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. The steps below shows you how to run it on our Whitehead server. 
+  * 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. 
       * content in input sample.json: