diff ICGC_STAR_ALIGNMENT_PIPELINE/ICGC_pipeline.sh @ 0:0446d6f7d593 draft default tip

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ICGC_STAR_ALIGNMENT_PIPELINE/ICGC_pipeline.sh	Wed Apr 18 02:38:42 2018 -0400
@@ -0,0 +1,51 @@
+#!/bin/bash
+
+if [ "$#" -ne 1 ]; then
+ echo "[usage:] ICGC_pipeline.sh  fastq_in_tar.gz"
+ exit 1;
+fi
+
+#FASTQ_1=$1
+#FASTQ_2=$2
+#SAMPLE_ID=$3
+#TAR_FILE=$SAMPLE_ID".tar"
+TAR_FILE=$1
+
+export PATH=/storage/data/program/GDC_TGCA-Harmonized/RNA-Seq/bin/ICGC-STAR_ALIGNMENT_PIPELINE:$PATH
+
+#tar cvfh $TAR_FILE  $FASTQ_2  $FASTQ_1 
+
+STAD_ALIGN=~/package/DAUMSOFT/RNA-seq/ICGC_STAR_ALIGNMENT_PIPELINE/star_align.py
+STAR_INDEX_PATH=~/refs/hg38/gdc/Index_Files/GDC.h38.d1.vd1_STAR2_Index_Files/star_genome_d1_vd1_gtfv22
+WORK_DIR=./wrk
+OUTPUT_BAM=./out
+REFERENCE=~/refs/hg38/gdc/GRCh38.d1.vd1_Reference_Sequence/GRCh38.d1.vd1.fa
+RUN_THREAD_NUM=8
+rm -rf $WORK_DIR
+rm -rf $OUTPUT_BAM
+mkdir $WORK_DIR
+mkdir $OUTPUT_BAM
+
+python $STAD_ALIGN              \
+--genomeDir $STAR_INDEX_PATH    \
+--tarFileIn $TAR_FILE  \
+--workDir $WORK_DIR             \
+--out $OUTPUT_BAM \
+--genomeFastaFiles $REFERENCE \
+--runThreadN $RUN_THREAD_NUM \
+--outFilterMultimapScoreRange 1 \
+--outFilterMultimapNmax 20 \
+--outFilterMismatchNmax 10 \
+--alignIntronMax 500000 \
+--alignMatesGapMax 1000000 \
+--sjdbScore 2 \
+--limitBAMsortRAM 0 \
+--alignSJDBoverhangMin 1 \
+--genomeLoad NoSharedMemory \
+--outFilterMatchNminOverLread 0.33 \
+--outFilterScoreMinOverLread 0.33 \
+--twopass1readsN -1 \
+--sjdbOverhang 100 \
+--outSAMstrandField intronMotif \
+--outSAMunmapped Within
+