Permalink
Browse files
Small tweaks to reduce disk usage. Do not write unpaired fastq files …
- Loading branch information...
Showing
with
5 additions
and
5 deletions.
-
BIN
tools/AutoADAG.pyc
-
+1
−1
tools/StringTie
-
+2
−2
tools/hisat2
-
+2
−2
tools/tophat
|
|
@@ -38,7 +38,7 @@ if [ $COUNT = 0 ]; then |
|
|
exit 0
|
|
|
fi
|
|
|
|
|
|
-stringtie *.bam -G $GFF3 -e -B -o out.gtf
|
|
|
+stringtie *.bam -G $GFF3 -e -B > /dev/null
|
|
|
|
|
|
python ST_ttab_parse.py t_data.ctab > $BASE_NAME-merged_counts.fpkm
|
|
|
|
|
|
@@ -31,8 +31,8 @@ if [ $LAYOUT = "paired" ] ; then |
|
|
java -Xmx512m \
|
|
|
-jar trimmomatic-0.36.jar PE -threads 1 -phred33 \
|
|
|
$BASE_NAME-forward-$COMMON_NAME $BASE_NAME-reverse-$COMMON_NAME \
|
|
|
- left_result.paired_trim.forward_$COMMON_NAME.fastq left_result.unpaired_trim.forward_$COMMON_NAME.fastq \
|
|
|
- right_result.paired_trim.reverse_$COMMON_NAME.fastq right_result.unpaired_trim.reverse_$COMMON_NAME.fastq \
|
|
|
+ left_result.paired_trim.forward_$COMMON_NAME.fastq /dev/null \
|
|
|
+ right_result.paired_trim.reverse_$COMMON_NAME.fastq /dev/null \
|
|
|
ILLUMINACLIP:fasta_adapter.txt:2:40:15 LEADING:3 TRAILING:6 SLIDINGWINDOW:4:15 MINLEN:50 \
|
|
|
2>&1 | tee $BASE_NAME-$COMMON_NAME-trimmomatic.txt
|
|
|
|
|
|
|
|
|
@@ -33,8 +33,8 @@ if [ $LAYOUT = "paired" ] ; then |
|
|
java -Xmx512m \
|
|
|
-jar trimmomatic-0.36.jar PE -threads 1 -phred33 \
|
|
|
$BASE_NAME-forward-$COMMON_NAME $BASE_NAME-reverse-$COMMON_NAME \
|
|
|
- left_result.paired_trim.forward_$COMMON_NAME.fastq left_result.unpaired_trim.forward_$COMMON_NAME.fastq \
|
|
|
- right_result.paired_trim.reverse_$COMMON_NAME.fastq right_result.unpaired_trim.reverse_$COMMON_NAME.fastq \
|
|
|
+ left_result.paired_trim.forward_$COMMON_NAME.fastq /dev/null \
|
|
|
+ right_result.paired_trim.reverse_$COMMON_NAME.fastq /dev/null \
|
|
|
ILLUMINACLIP:fasta_adapter.txt:2:40:15 LEADING:3 TRAILING:6 SLIDINGWINDOW:4:15 MINLEN:50 \
|
|
|
2>&1 | tee $BASE_NAME-$COMMON_NAME-trimmomatic.txt
|
|
|
|
|
|
|
0 comments on commit
4e0bb40