Changes between Version 31 and Version 32 of SOPs/atac_Seq

Timestamp:

10/27/20 14:52:39 (4 years ago)

Author:

byuan

Comment:

--

SOPs/atac_Seq

@@ -90 +90 @@
 # --peak-file: peak file in bed format
 # --tss-file: tss in bed format
-# --excluded-region-file A BED file containing excluded regions, in this case, we exclude the regions in the ENCODE blast list
+# --excluded-region-file A bed file containing excluded regions, in this case, we exclude the regions in the ENCODE blast list
 # --metrics-file: output in json format
 # --ignore-read-groups: Even if read groups are present in the BAM file, ignore them and combine metrics for all reads under a single sample and library named with the --name option. This also implies that a single peak file will be used for all reads. 
+
 # The duplicated reads need to be labeled by Picard MarkDuplicates ( REMOVE_DUPLICATES=FALSE) before running the ataqv
-# ataqc supports human/mouse/rat/fly/worm/yeast currently. If your genome is not listed, you can run it with --autosomal-reference-file and --mitochondrial-reference-name
+
+# ataqc supports human/mouse/rat/fly/worm/yeast currently. If your genome is not listed, you can still run it by adding --autosomal-reference-file and --mitochondrial-reference-name.
 #    --autosomal-reference-file: a file containing autosomal reference names, one per line
 #    --mitochondrial-reference-name: name for the mitochondrial DNA