From b6b55663d90609fd1657090a62d808795c73eca5 Mon Sep 17 00:00:00 2001
From: wbaopaul <yuw1@email.chop.edu>
Date: Fri, 4 Mar 2022 09:59:15 -0500
Subject: [PATCH] minor modification in mapping_qc

---
 README.md                  | 2 +-
 scATAC-pro.wiki            | 2 +-
 scripts/cell_mapping_qc.sh | 9 ++++++---
 scripts/mapping_qc.sh      | 9 ++++++---
 4 files changed, 14 insertions(+), 8 deletions(-)

diff --git a/README.md b/README.md
index e0b9e26..f6efe7a 100644
--- a/README.md
+++ b/README.md
@@ -155,7 +155,7 @@ Step by step guide to running scATAC-pro
 
 -   **IMPORTANT**: you can run scATAC-pro sequentially. The input of a later analysis module is the output of the previous analysis modules. The following tutorial uses fastq files downloaded from [PBMC10k 10X Genomics](https://support.10xgenomics.com/single-cell-atac/datasets/1.1.0/atac_v1_pbmc_10k?) 
     
--   <u>Run scATAC-pro sequentially (specifyi PEAK_CALLER = MACS2 and CELL_CALLER = FILTER or other values in the configure_user.txt file) </u>
+-   <u>Run scATAC-pro sequentially (specify PEAK_CALLER = MACS2 and CELL_CALLER = FILTER or other values in the configure_user.txt file) </u>
 
 ```
     $ scATAC-pro -s demplx_fastq 
diff --git a/scATAC-pro.wiki b/scATAC-pro.wiki
index f0da625..f8cac58 160000
--- a/scATAC-pro.wiki
+++ b/scATAC-pro.wiki
@@ -1 +1 @@
-Subproject commit f0da625acd87658f1d4520f2a78b74f2ad59f38c
+Subproject commit f8cac58c44a6266ce8cd3b2a615fcb9c646c1aad
diff --git a/scripts/cell_mapping_qc.sh b/scripts/cell_mapping_qc.sh
index f2c78be..988a226 100755
--- a/scripts/cell_mapping_qc.sh
+++ b/scripts/cell_mapping_qc.sh
@@ -46,9 +46,12 @@ tmp_bam_file=${output_dir}/tmp.bam
 
 
 if [[ $MAPPING_METHOD == bwa ]]; then
-    ${SAMTOOLS_PATH}/samtools view -@ $ncore -q 5 -f $flag0 -b ${input_pre}.bam > $tmp_bam_file
-   total_uniq_mapped=$( ${SAMTOOLS_PATH}/samtools view -c $tmp_bam_file )  ## number of unique mapped reads
-    rm $tmp_bam_file
+    #${SAMTOOLS_PATH}/samtools view -@ $ncore -q 5 -f $flag0 -b ${input_pre}.bam > $tmp_bam_file
+    #total_uniq_mapped=$( ${SAMTOOLS_PATH}/samtools view -c $tmp_bam_file )  ## number of unique mapped reads
+    #rm $tmp_bam_file
+    
+    ## alternatively
+    total_uniq_mapped=$( ${SAMTOOLS_PATH}/samtools view -q 1 -@ $ncore -f $flag0 ${input_pre}.bam | grep -v XA: | wc -l )
 else
     ${SAMTOOLS_PATH}/samtools view -@ $ncore -q 5 -f $flag0 ${input_pre}.bam > $tmp_sam_file
    total_uniq_mapped=$( grep -E "@|NM:" $tmp_sam_file | grep -v "XS:" | wc -l )
diff --git a/scripts/mapping_qc.sh b/scripts/mapping_qc.sh
index 1823bd2..1a3b08c 100755
--- a/scripts/mapping_qc.sh
+++ b/scripts/mapping_qc.sh
@@ -41,9 +41,12 @@ tmp_sam_file=${output_dir}/tmp.sam
 tmp_bam_file=${output_dir}/tmp.bam
 
 if [ $MAPPING_METHOD == 'bwa' ]; then
-    ${SAMTOOLS_PATH}/samtools view -@ $ncore -q 5 -f $flag0 -b ${input_pre}.positionsort.bam > $tmp_bam_file
-   total_uniq_mapped=$( ${SAMTOOLS_PATH}/samtools view -c $tmp_bam_file )  ## number of unique mapped reads
-    rm $tmp_bam_file
+    #${SAMTOOLS_PATH}/samtools view -@ $ncore -q 5 -f $flag0 -b ${input_pre}.positionsort.bam > $tmp_bam_file
+    #total_uniq_mapped=$( ${SAMTOOLS_PATH}/samtools view -c $tmp_bam_file )  ## number of unique mapped reads
+    #rm $tmp_bam_file
+   
+    ## alternatively
+    total_uniq_mapped=$( ${SAMTOOLS_PATH}/samtools view -q 1 -@ $ncore -f $flag0 ${input_pre}.positionsort.bam | grep -v XA: | wc -l )
 else
     ${SAMTOOLS_PATH}/samtools view -@ $ncore -q 5 -f $flag0 ${input_pre}.positionsort.bam > $tmp_sam_file
    total_uniq_mapped=$( grep -E "@|NM:" $tmp_sam_file | grep -v "XS:" | wc -l )