Changes between Version 64 and Version 65 of SOPs/atac_Seq

Timestamp:

06/15/21 14:17:04 (4 years ago)

Author:

byuan

Comment:

--

SOPs/atac_Seq

@@ -118 +118 @@
 MACS v2 is applicable for ATAC-Seq using the appropriate options/parameters. 
 
-  * Run [[https://github.com/ENCODE-DCC/atac-seq-pipeline|ENCODE ATAC-seq Pipeline]] . It works well with human (hg38, hg19) and mouse (mm10, mm9) samples with biological replicates. 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/|workflow]].  In addition, it does quality controls. The steps below shows you how to run it on our Whitehead server. 
-
-       * Verify there is no preexisting conda startup code with the command below:
-{{{
-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
-
-      * Ignore the developer's instructions, use your home directory for conda and the pipeline.
-{{{
-# Be sure to keep the first dot in the command below:
-. /nfs/BaRC_Public/conda/start_barc_conda
-conda activate encode-atac-seq-pipeline
-}}}
-
-      * Run. Files could be url or fullpath. [[https://github.com/ENCODE-DCC/atac-seq-pipeline/blob/master/docs/input.md | Detail information about .json file]]
-{{{
-caper run /nfs/BaRC_Public/atac-seq-pipeline/atac.wdl -i sample.json
-# After the job finishes, you can deactivate conda with
-conda deactivate
-}}}
-
-
+  * 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/|workflow]].  In addition, it does quality controls. The steps below shows you how to run it on our Whitehead server. 
       * content in sample.json:
 
@@ -172 +150 @@
           * mm10: /nfs/BaRC_datasets/ENCODE_ATAC-seq_Pipeline/mm10/mm10.tsv
 
+       * Before running ENCODE pipeline, verify there is no preexisting conda startup code with the command below:
+{{{
+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
+
+      * Ignore the developer's instructions, use your home directory for conda and the pipeline.
+{{{
+# Be sure to keep the first dot in the command below:
+. /nfs/BaRC_Public/conda/start_barc_conda
+conda activate encode-atac-seq-pipeline
+}}}
+
+      * Run. Files could be url or fullpath. [[https://github.com/ENCODE-DCC/atac-seq-pipeline/blob/master/docs/input.md | Detail information about .json file]]
+{{{
+caper run /nfs/BaRC_Public/atac-seq-pipeline/atac.wdl -i sample.json
+# After the job finishes, you can deactivate conda with
+conda deactivate
+}}}