Changes between Version 14 and Version 15 of SOPs/atac_Seq

Timestamp:

08/14/20 12:19:48 (4 years ago)

Author:

gbell

Comment:

--

SOPs/atac_Seq

@@ -29 +29 @@
 === [=#preprocess Map reads] ===
 
-  * Map reads with bowtie2, 
+  * Map reads with bowtie2 (or another unspliced mapping tool) 
   * If mapping paired-end reads, keep only concordant pairs
 
@@ -46 +46 @@
 {{{
 samtools view -h file.bam | grep -v chrM | samtools view -b -h -f 0x2 - | samtools sort - > file.sorted.bam
+}}}
+
+=== [=#QC Run quality control and calculate QC metrics] ===
+
+Calculate the fragment size distribution with the ATACseqQC R package:
+{{{
+library("ATACseqQC")
+pdf("My_sample.fragment_sizes.pdf", sep="_"), w=11, h=8.5)
+fragSizeDist("Mapped_reads.bam", "My_sample")
+dev.off()
+}}}
+
+Calculate the TSS enrichment score (the degree to which transcription start sites show enrichment for ATAC-seq reads) using BaRC code (/nfs/BaRC_Public/BaRC_code/Python/calculate_TSS_enrichment_score/calculate_TSS_enrichment_score.py)
+{{{
+# USAGE: calculate_TSS_enrichment_score.py --outdir OUTDIR --outprefix OUTPREFIX --fastq1 FASTQ1 --tss TSS_BED --chromsizes CHROMSIZES --bam BAM
+
+./calculate_TSS_enrichment_score.py --outdir OUT_QC_1 --outprefix Sample_A --fastq1 ATACseq_reads.fq.gz --tss TSS.hg38.bed --chromsizes chromInfo.hg38.txt --bam ATACseq_mapped_reads.bam >| Sample_A.TSS_enrichment_score.txt
 }}}
 
@@ -87 +104 @@
 }}}
 
+Calculate the FRiP score
+{{{
+/nfs/BaRC_Public/BaRC_code/Python/calculate_FRiP_score/calculate_FRiP_score.py
+}}}
+
 
 === Tips/Recommendations for ATAC-Seq ===
@@ -106 +128 @@
 
 
-=== [=#QC Run quality control and calculate QC metrics] ===
-
-* Fragment size distribution with ATACseqQC R package:
-{{{
-library("ATACseqQC")
-
-bamfile = "foo.bam"
-bamfile.labels <- gsub(".bam", "", basename(bamfile))
-
-pdf (file=paste(bamfile.labels, "Fragment_size.pdf", sep="_"), w=11, h=8.5)
-fragSizeDist(bamfile, bamfile.labels)
-dev.off()
-
-}}}