Changes between Version 82 and Version 83 of SOPs/atac_Seq

Timestamp:

07/09/21 13:54:42 (4 years ago)

Author:

gbell

Comment:

--

SOPs/atac_Seq

@@ -49 +49 @@
 }}}
 
-  * Remove reads with low quality score: MAPQ < 30 with alignmentSieve from [[https://deeptools.readthedocs.io/en/develop/|DeepTools]]
-{{{
-alignmentSieve -b file.bam --minMappingQuality 30 --samFlagInclude 2 -o MAPQ30.bam"
-#samFlagInclude 2 is used to keep only properly paired reads
+  * Remove reads with low quality score: MAPQ < 30
+{{{
+# Use alignmentSieve from [[https://deeptools.readthedocs.io/en/develop/|DeepTools]]
+#   "--samFlagInclude 2" => keep only properly paired reads
+alignmentSieve -b file.bam --minMappingQuality 30 --samFlagInclude 2 -o MAPQ30.bam
+
+# Use samtools (for single-end reads)
+samtools view -b -q 30 file.bam > MAPQ30.bam
 }}}