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starMono2.sh
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starMono2.sh
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#!/bin/bash
#SBATCH -J RNAseq
#SBATCH -o %x.out
#SBATCH -n 12
#SBATCH --mem-per-cpu=18000
if [ "$1" = "help" ] || [ -z $1 ]; then
echo ""
echo "--------------------------------------------------------------------------------------"
echo " To run this script, use the following syntax:"
echo " bash" $0 "<delim> <fastqFile> <genomeDirPath>"
echo ""
echo " NOTE: this script retains unmapped reads + spits unmapped fastq's"
echo "--------------------------------------------------------------------------------------"
echo ""
echo "******************************************** "
echo "**********/ EXTENDED GENOME LIST /********** "
echo "[hg38]=/workdir/genomes/Homo_sapiens/hg38/UCSC/hg38.star "
echo "[mm10]=/workdir/genomes/Mus_musculus/mm10/UCSC/mm10.star "
echo "[GRCh38]=/workdir/genomes/Homo_sapiens/hg38/ENSEMBL/GRCh38.star "
echo "[GRCm38]=/workdir/genomes/Mus_musculus/mm10/ENSEMBL/GRCm38.star "
echo "[cat]=/workdir/genomes/Felis_catus/Felis_catus9.0/Ensembl/genomeDir "
echo "[chicken]=/workdir/genomes/Gallus_gallus/Galgal5/ENSEMBL/galgal5.star "
echo "[horse]=/workdir/genomes/Equus_caballus/ENSEMBL/Equus_caballus.star "
echo "[rat]=/workdir/genomes/Rattus_norvegicus/rn6/ENSEMBL/rat.star "
echo "[ercc]=/workdir/genomes/contaminants/ERCC_spikeIns/ercc.star "
echo "[lonchura]=/workdir/genomes/Lonchura_striata/LonStrDom1/ENSEMBL/lonchura.star "
echo "[goose]=/workdir/genomes/Anser_brachyrhynchus/ASM259213v1/ENSEMBL/goose.star "
echo "[ehv8]=/workdir/genomes/FastQ_Screen_Genomes/EHV8/ehv8.star "
echo "[erdman]=/workdir/genomes/Mycobacterium_tuberculosis/Ensembl_GCA_000668235/GCA_000668235.star "
echo "[TB]=/workdir/genomes/Mycobacterium_tuberculosis/CDC1551_Ensembl/cdc1551.star "
echo "[maize]=/workdir/genomes/Zea_mays/B73_RefGen_v4/ENSEMBL/star.maize "
echo "[finch]=/workdir/genomes/Taeniopygia_guttata/taeGut3.2.4/ENSEMBL/star.index "
echo "[dog]=/workdir/genomes/Canis_familiaris/canFam3/ENSEMBL/star.index "
exit 1
else
#--outSAMunmapped Within \
DELIMITER=`echo $1 | cut -d , -f1`
FIELD=`echo $1 | cut -d , -f2-`
iSUB=`echo $i | cut -d ${DELIMITER} -f${FIELD}`
STAR \
--runThreadN 12 \
--genomeDir $3 \
--readFilesIn $2 \
--readFilesCommand gunzip -c \
--outSAMstrandField intronMotif \
--outReadsUnmapped Fastx \
--outFilterIntronMotifs RemoveNoncanonical \
--outSAMtype BAM SortedByCoordinate \
--outFileNamePrefix ${iSUB}. \
--limitBAMsortRAM 61675612266 \
--quantMode GeneCounts
fi