From c0793ad629acb3144534a4c72a2cdb71765cac3f Mon Sep 17 00:00:00 2001
From: Brandi Cantarel <brandi.cantarel@utsouthwestern.edu>
Date: Fri, 9 Nov 2018 20:10:45 -0600
Subject: [PATCH] update alignment bug
---
alignment/rnaseqalign.sh | 3 ++-
1 file changed, 2 insertions(+), 1 deletion(-)
diff --git a/alignment/rnaseqalign.sh b/alignment/rnaseqalign.sh
index 8feea1b..8eaab50 100644
--- a/alignment/rnaseqalign.sh
+++ b/alignment/rnaseqalign.sh
@@ -69,8 +69,9 @@ else
else
samtools view -1 --threads $SLURM_CPUS_ON_NODE -o output.bam out.sam
fi
- samtools sort -@ $SLURM_CPUS_ON_NODE -O BAM -n -o output.nsort.bam output.bam
+ samtools sort -@ $SLURM_CPUS_ON_NODE -O BAM -o ${pair_id}.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
+
fi
samtools index -@ $SLURM_CPUS_ON_NODE ${pair_id}.bam
--
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