Changes between Version 77 and Version 78 of SOPs/atac_Seq

Timestamp:

07/09/21 11:03:40 (4 years ago)

Author:

byuan

Comment:

--

SOPs/atac_Seq

@@ -47 +47 @@
 }}}
 
-  * Remove reads mapped to mitochondria.
-{{{
-samtools view -h file.bam | grep -v chrM | samtools view -b -h -f 0x2 - | samtools sort - > file.sorted.bam
-}}}
   * Remove reads with low quality score: MAPQ < 30 with alignmentSieve from [[https://deeptools.readthedocs.io/en/develop/|DeepTools]]
 {{{
@@ -63 +59 @@
   * Check deduplication level with [[http://barcwiki.wi.mit.edu/wiki/SOPs/qc_shortReads | 'fastqc']].
  
-
+  * Remove reads mapped to mitochondria.
+{{{
+samtools view -h file.bam | grep -v chrM | samtools view -b -h -f 0x2 - | samtools sort - > file.sorted.bam
+}}}
 
 === [=#call_peaks Call peaks] ===