Changes between Version 28 and Version 29 of SOPs/atac_Seq

Timestamp:

10/27/20 14:45:59 (5 years ago)

Author:

byuan

Comment:

--

SOPs/atac_Seq

@@ -79 +79 @@
 
 The [https://www.encodeproject.org/atac-seq/#standards ENCODE project] has some recommended TSS enrichment scores, depending on the genome.
+
+In addition to do varies quality controls, [[ https://www.sciencedirect.com/science/article/pii/S240547122030079X | ataqv ]] summarizes QC results into an interactive html page, which also allows you to view multiple samples together. 
+
+First, run ataqv on each bam file to generate JSON files.
+Here is a sample command for a bulk ATAC_seq sample:
+
+
+{{{
+
+# --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
+# --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
+#    --autosomal-reference-file: a file containing autosomal reference names, one per line
+#    --mitochondrial-reference-name: name for the mitochondrial DNA
+
+ataqv --peak-file sample1_peak.bed --name sample1 --metrics-file sample1.ataqv.json.gz --excluded-region-file /nfs/genomes/human_hg38_dec13/anno/hg38-blacklist.v2.bed.gz --tss-file hg38.tss.refseq.bed.gz --ignore-read-groups human sample1.bam > sample1.ataqv.out”
+
+}}}
+
+
+Run mkarv on the JSON files to generate the interactive web viewer. By default, SRR891268 will be used as the reference sample in the viewer. You can specify a different reference when you built your viewer instance, refer to the information on how to configure the reference with mkarv -h.
+
+{{{
+
+# This will create a folder named as sample1, whose index.html contains the interactive plots. 
+mkarv sample1 sample1.ataqv.json.gz
+
+# I you have multiple samples, you can combine them into a single report. In this case, both sample1 and sample2 will be in the same plots inside folder called "all_samples"
+mkarv all_samples sample1.ataqv.json.gz sample2.ataqv.json.gz 
+
+}}}
+
 
 === [=#call_peaks Call peaks] ===