Changes between Version 20 and Version 21 of SOPs/atac_Seq

Timestamp:

09/22/20 10:27:16 (4 years ago)

Author:

byuan

Comment:

--

SOPs/atac_Seq

@@ -95 +95 @@
 samtools sort -n bowtie/ATAC.bam > ATAC_sortedByName.bam
 # Run Genrich
-Genrich -e chrM -j -r -v -t ATAC_sortedByName.bam -o peaks/ATAC_peak -f peaks/ATAC_log
+Genrich -e chrM -j -r -m 30 -v -t ATAC_sortedByName.bam -o peaks/ATAC_peak -f peaks/ATAC_log
 
 where
 -j              ATAC-seq mode (must be specified)  intervals are interpreted that are centered on transposase cut sites (the ends of each DNA fragment). Only properly paired alignment are analyzed by default
 -r              Remove PCR duplicates
+-m  <int>       Minimum MAPQ to keep an alignment (def. 0)
 -d <int>        Expand cut sites to the given length (default 100bp)
 -e <arg>        Chromosomes (reference sequences) to exclude. Can be a comma-separated  list, e.g. -e chrM,chrY.