Changes between Version 54 and Version 55 of SOPs/atac_Seq

Timestamp:

06/07/21 18:07:42 (4 years ago)

Author:

thiruvil

Comment:

--

SOPs/atac_Seq

@@ -48 +48 @@
   * Remove reads with low quality score: MAPQ < 30 with alignmentSieve from [[https://deeptools.readthedocs.io/en/develop/|DeepTools]]
 {{{
-alignmentSieve -b file.bam --minMappingQuality 30 -o MAPQ30.bam"
+alignmentSieve -b file.bam --minMappingQuality 30 --samFlagInclude 2 -o MAPQ30.bam"
+#samFlagInclude 2 is used to keep only properly paired reads
 }}}