From ba64b4b12f6cac012c9af7f874489bea9421f13c Mon Sep 17 00:00:00 2001
From: Brandi Cantarel <brandi.cantarel@utsouthwestern.edu>
Date: Thu, 22 Mar 2018 15:35:22 -0500
Subject: [PATCH] update umi support rnaseqalign
---
alignment/rnaseqalign.sh | 15 ++++++++-------
1 file changed, 8 insertions(+), 7 deletions(-)
diff --git a/alignment/rnaseqalign.sh b/alignment/rnaseqalign.sh
index 52de23a..b86be37 100644
--- a/alignment/rnaseqalign.sh
+++ b/alignment/rnaseqalign.sh
@@ -34,7 +34,7 @@ if [[ -z $pair_id ]] || [[ -z $fq1 ]]; then
fi
source /etc/profile.d/modules.sh
-module load samtools/gcc/1.6 picard/2.10.3
+module load samtools/1.6 picard/2.10.3
baseDir="`dirname \"$0\"`"
if [[ -z $SLURM_CPUS_ON_NODE ]]
then
@@ -59,13 +59,14 @@ else
else
hisat2 -p $SLURM_CPUS_ON_NODE --rg-id ${pair_id} --rg LB:tx --rg PL:illumina --rg PU:barcode --rg SM:${pair_id} --add-chrname --no-unal --dta -x ${index_path}/hisat_index/genome -1 $fq1 -2 $fq2 -S out.sam --summary-file ${pair_id}.alignerout.txt
fi
- samtools view -1 --threads $SLURM_CPUS_ON_NODE -o output.bam out.sam
-fi
-if [[ $umi==1 ]]
-then
- python ${baseDir}/add_umi_bam.py -b output.bam -o output.unsort2.bam
- mv output.unsort2.bam output.bam
+ if [[ $umi==1 ]]
+ then
+ python ${baseDir}/add_umi_sam.py -s out.sam -o output.bam
+ else
+ samtools view -1 --threads $SLURM_CPUS_ON_NODE -o output.bam out.sam
+ fi
fi
+
samtools sort -@ $SLURM_CPUS_ON_NODE -O BAM -n -o output.nsort.bam output.bam
java -jar $PICARD/picard.jar FixMateInformation ASSUME_SORTED=TRUE SORT_ORDER=coordinate ADD_MATE_CIGAR=TRUE I=output.nsort.bam O=${pair_id}.bam
samtools index -@ $SLURM_CPUS_ON_NODE ${pair_id}.bam
--
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