Changes between Version 11 and Version 12 of SOPs/atac_Seq

Timestamp:

08/14/20 11:11:03 (4 years ago)

Author:

byuan

Comment:

--

SOPs/atac_Seq

@@ -8 +8 @@
  * [#preprocess Pre-process reads](remove adapters and other "contamination")
  * [#map Map reads to the genome] (with an unspliced mapping tool)
- * Run quality control and calculate QC metrics
+ * [#Run quality control and calculate QC metrics]
  * [#call_peaks Call ATAC-seq "peaks"] with a high coverage of mapped reads
  * Analyze peak regions for binding motifs
@@ -106 +106 @@
 
 
+=== [=#Run quality control and calculate QC metrics] ===
+* Fragment size distribution with ATACseqQC R package:
+{{{
+library("ATACseqQC")
 
+bamfile = "foo.bam"
+bamfile.labels <- gsub(".bam", "", basename(bamfile))
 
+pdf (file=paste(bamfile.labels, "Fragment_size.pdf", sep="_"), w=11, h=8.5)
+fragSizeDist(bamfile, bamfile.labels)
+dev.off()
+
+}}}