Changes between Version 74 and Version 75 of SOPs/atac_Seq

Timestamp:

07/09/21 08:57:44 (4 years ago)

Author:

gbell

Comment:

--

SOPs/atac_Seq

@@ -17 +17 @@
 === [=#preprocess Pre-process reads] ===
 
-  * Check adapter contamination with fastqc. Remove adapters with cutadapt or trim_galore.  Since many ATAC-seq experiments use the Nextera DNA Library Prep Kit, one commonly needs to trim Nextera adapters.
-
-{{{
-# --fastqc                Run FastQC in the default mode on the FastQ file once trimming is complete.
-# --nextera               Nextera adapter is commonly used for ATAC-seq
-                          Adapter sequence to be trimmed is the first 12bp of the Nextera adapter
+  * Check adapter contamination with fastqc. Remove adapters with cutadapt or trim_galore.  
+
+{{{
+# --fastqc                Run FastQC in the default mode on the fastq file once trimming is complete.
+# --nextera               Adapter sequence to be trimmed is the first 12bp of the Nextera adapter
                           'CTGTCTCTTATA' instead of the default auto-detection of adapter sequence.
+                          Since many ATAC-seq experiments use the Nextera DNA Library Prep Kit, 
+                          one commonly needs to trim Nextera adapters.
+# --paired                If reads are paired, both reads need to pass or they are both removed.
+# --length                Discard trimmed reads shorter than this length.
+
 trim_galore --fastqc  -nextera --paired --length 30 -o clean_adaptor_folder read1.fq read2.fq
 }}}