From b54812cf50ad27dfd68edb4bb3dc59aead7a4187 Mon Sep 17 00:00:00 2001
From: Brandi Cantarel <brandi.cantarel@utsouthwestern.edu>
Date: Mon, 26 Mar 2018 09:20:34 -0500
Subject: [PATCH] update support single-end
---
alignment/rnaseqalign.sh | 11 +++++++----
preproc_fastq/trimgalore.sh | 10 +++++-----
2 files changed, 12 insertions(+), 9 deletions(-)
diff --git a/alignment/rnaseqalign.sh b/alignment/rnaseqalign.sh
index 52de23a..ecee18b 100644
--- a/alignment/rnaseqalign.sh
+++ b/alignment/rnaseqalign.sh
@@ -40,9 +40,12 @@ if [[ -z $SLURM_CPUS_ON_NODE ]]
then
SLURM_CPUS_ON_NODE=1
fi
+
+diff $fq1 $fq2 > difffile.out
+
if [ $algo == 'star' ]
then
- if ($fq1 != $fq2)
+ 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
@@ -53,11 +56,11 @@ then
mv outAligned.sortedByCoord.out.bam output.bam
else
module load hisat2/2.1.0-intel
- if [ $fq1 == $fq2 ]
+ if [ -s difffile ]
then
- 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 -U $fq1 -S out.sam --summary-file ${pair_id}.alignerout.txt
- 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
+ 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 -U $fq1 -S out.sam --summary-file ${pair_id}.alignerout.txt
fi
samtools view -1 --threads $SLURM_CPUS_ON_NODE -o output.bam out.sam
fi
diff --git a/preproc_fastq/trimgalore.sh b/preproc_fastq/trimgalore.sh
index b941ef1..1ae8ba1 100644
--- a/preproc_fastq/trimgalore.sh
+++ b/preproc_fastq/trimgalore.sh
@@ -32,13 +32,13 @@ r2base="${fq2%.fastq*}"
source /etc/profile.d/modules.sh
module load trimgalore/0.4.1 cutadapt/1.9.1
-if [ $fq1 == $fq2 ]
+if [ -s $fq2 ]
then
- trim_galore -q 25 --illumina --gzip --length 35 ${fq1}
- mv ${r1base}_trimmed.fq.gz ${pair_id}.trim.R1.fastq.gz
- cp ${pair_id}.trim.R1.fastq.gz ${pair_id}.trim.R2.fastq.gz
-else
trim_galore --paired -q 25 --illumina --gzip --length 35 ${fq1} ${fq2}
mv ${r1base}_val_1.fq.gz ${pair_id}.trim.R1.fastq.gz
mv ${r2base}_val_2.fq.gz ${pair_id}.trim.R2.fastq.gz
+else
+ trim_galore -q 25 --illumina --gzip --length 35 ${fq1}
+ mv ${r1base}_trimmed.fq.gz ${pair_id}.trim.R1.fastq.gz
+ cp ${pair_id}.trim.R1.fastq.gz ${pair_id}.trim.R2.fastq.gz
fi
--
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