From 0bdf56d5bdb9252ce418fcf7d0c7bdbcee9ff4a1 Mon Sep 17 00:00:00 2001
From: Brandi Cantarel <brandi.cantarel@utsouthwestern.edu>
Date: Tue, 17 Apr 2018 17:41:16 -0500
Subject: [PATCH] fixed all issues with STAR -- still a crappy aligner
nontheless
---
alignment/rnaseqalign.sh | 8 ++++----
1 file changed, 4 insertions(+), 4 deletions(-)
diff --git a/alignment/rnaseqalign.sh b/alignment/rnaseqalign.sh
index ed85697..8fea8af 100644
--- a/alignment/rnaseqalign.sh
+++ b/alignment/rnaseqalign.sh
@@ -45,7 +45,7 @@ diff $fq1 $fq2 > difffile.out
if [ $algo == 'star' ]
then
- if (-s difffile)
+ if [ -s difffile ]
then
module load star/2.4.2a
STAR --genomeDir ${index_path}/star_index/ --readFilesIn $fq1 $fq2 --readFilesCommand zcat --genomeLoad NoSharedMemory --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outSAMheaderCommentFile COfile.txt --outSAMheaderHD @HD VN:1.4 SO:coordinate --outSAMunmapped Within --outFilterType BySJout --outSAMattributes NH HI AS NM MD --outSAMstrandField intronMotif --outSAMtype BAM SortedByCoordinate --quantMode TranscriptomeSAM --sjdbScore 1 --limitBAMsortRAM 60000000000 --outFileNamePrefix out
@@ -54,7 +54,7 @@ then
STAR --genomeDir ${index_path}/star_index/ --readFilesIn $fq1 --readFilesCommand zcat --genomeLoad NoSharedMemory --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outSAMheaderCommentFile COfile.txt --outSAMheaderHD @HD VN:1.4 SO:coordinate --outSAMunmapped Within --outFilterType BySJout --outSAMattributes NH HI AS NM MD --outSAMstrandField intronMotif --outSAMtype BAM SortedByCoordinate --quantMode TranscriptomeSAM --sjdbScore 1 --limitBAMsortRAM 60000000000 --outFileNamePrefix out
fi
mv outLog.final.out ${pair_id}.alignerout.txt
- mv outAligned.sortedByCoord.out.bam output.bam
+ mv outAligned.sortedByCoord.out.bam ${pair_id}.bam
else
module load hisat2/2.1.0-intel
if [ -s difffile ]
@@ -69,8 +69,8 @@ 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
+ 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 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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