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script_alignment.sh
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## originally by Yulong Niu
date
REF_PATH=/netscratch/dep_psl/grp_rgo/yniu/ref/ath
CLEAN_PATH=/netscratch/dep_psl/grp_rgo/yniu/KaWaiFlg22/clean_data_1stadd
ALIGN_PATH=/netscratch/dep_psl/grp_rgo/yniu/KaWaiFlg22/align_data_1stadd_virus1
KALLISTO_PATH=/home/yniu/Biotools/kallisto_v0.46.1
HISAT2_PATH=/home/yniu/Biotools/hisat2-2.1.0
SAMTOOL_PATH=/opt/share/software/bin
RM_PATH=/bin/rm
MOVE_PATH=/bin/mv
CORENUM=45
SPECIES='ath'
cd ${REF_PATH}
##~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~raw~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
fq=($(ls ${CLEAN_PATH} | grep .fq.gz))
fqnames=($(echo "${fq[@]%%.*}" | tr ' ' '\n' | sort -u | tr '\n' ' '))
for i in ${fqnames[@]}; do
echo "===================================="
echo "Kallisto using ${SPECIES} cDNA for ${i}."
${KALLISTO_PATH}/kallisto quant \
--genomebam \
--gtf ${REF_PATH}/Arabidopsis_thaliana.TAIR10.42.gtf.gz \
--chromosomes ${REF_PATH}/Arabidopsis_thaliana.TAIR10.dna.toplevel.fa.fai \
-t ${CORENUM} \
-i ${REF_PATH}/ath.kindex \
-o ${ALIGN_PATH}/${i}_${SPECIES}_kallisto \
--single -l 200 -s 20\
${CLEAN_PATH}/${i}.fq.gz
${MOVE_PATH} ${ALIGN_PATH}/${i}_${SPECIES}_kallisto/pseudoalignments.bam \
${ALIGN_PATH}/${i}_${SPECIES}_kallisto/${i}_${SPECIES}_pseudoalignments.bam
${MOVE_PATH} ${ALIGN_PATH}/${i}_${SPECIES}_kallisto/pseudoalignments.bam.bai \
${ALIGN_PATH}/${i}_${SPECIES}_kallisto/${i}_${SPECIES}_pseudoalignments.bam.bai
echo "HISAT2 using ${SPECIES} genome for ${i}."
${HISAT2_PATH}/hisat2 -p ${CORENUM} \
-x ${REF_PATH}/athht2index/genome \
-U ${CLEAN_PATH}/${i}.fq.gz \
-S ${ALIGN_PATH}/${i}_${SPECIES}_hisat2.sam
${SAMTOOL_PATH}/samtools sort \
-@ ${CORENUM} \
-o ${ALIGN_PATH}/${i}_${SPECIES}_hisat2.bam \
${ALIGN_PATH}/${i}_${SPECIES}_hisat2.sam
${SAMTOOL_PATH}/samtools index ${ALIGN_PATH}/${i}_${SPECIES}_hisat2.bam
${RM_PATH} ${ALIGN_PATH}/${i}_${SPECIES}_hisat2.sam
echo "====================================="
done
##~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
##~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~1stadd~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
fq=($(ls ${CLEAN_PATH} | grep .fq.gz))
fqnames=($(echo "${fq[@]%_*}" | tr ' ' '\n' | sort -u | tr '\n' ' '))
for i in ${fqnames[@]}; do
echo "===================================="
echo "Kallisto using ${SPECIES} cDNA for ${i}."
${KALLISTO_PATH}/kallisto quant \
-t ${CORENUM} \
-i ${REF_PATH}/ath.kindex \
-o ${ALIGN_PATH}/${i}_${SPECIES}_kallisto \
${CLEAN_PATH}/${i}_R1.fq.gz ${CLEAN_PATH}/${i}_R2.fq.gz
echo "HISAT2 using ${SPECIES} genome for ${i}."
${HISAT2_PATH}/hisat2 -p ${CORENUM} \
-x ${REF_PATH}/athht2index/genome \
-1 ${CLEAN_PATH}/${i}_R1.fq.gz \
-2 ${CLEAN_PATH}/${i}_R2.fq.gz \
-S ${ALIGN_PATH}/${i}_${SPECIES}_hisat2.sam
${SAMTOOL_PATH}/samtools sort \
-@ ${CORENUM} \
-o ${ALIGN_PATH}/${i}_${SPECIES}_hisat2.bam \
${ALIGN_PATH}/${i}_${SPECIES}_hisat2.sam
${SAMTOOL_PATH}/samtools index ${ALIGN_PATH}/${i}_${SPECIES}_hisat2.bam
${RM_PATH} ${ALIGN_PATH}/${i}_${SPECIES}_hisat2.sam
echo "====================================="
done
##~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
##~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~1stadd virus~~~~~~~~~~~~~~~~~~~~~~~~~~
fq=($(ls ${CLEAN_PATH} | grep .fq.gz))
fqnames=($(echo "${fq[@]%_*}" | tr ' ' '\n' | sort -u | tr '\n' ' '))
for i in ${fqnames[@]}; do
echo "===================================="
echo "Kallisto using ${SPECIES} cDNA for ${i}."
${KALLISTO_PATH}/kallisto quant \
-t ${CORENUM} \
-i ${REF_PATH}/ath_latentvirus1.kindex \
-o ${ALIGN_PATH}/${i}_${SPECIES}_kallisto \
${CLEAN_PATH}/${i}_R1.fq.gz ${CLEAN_PATH}/${i}_R2.fq.gz
echo "HISAT2 using ${SPECIES} genome for ${i}."
${HISAT2_PATH}/hisat2 -p ${CORENUM} \
-x ${REF_PATH}/athlatenvirus1ht2index/genome \
-1 ${CLEAN_PATH}/${i}_R1.fq.gz \
-2 ${CLEAN_PATH}/${i}_R2.fq.gz \
-S ${ALIGN_PATH}/${i}_${SPECIES}_hisat2.sam
${SAMTOOL_PATH}/samtools sort \
-@ ${CORENUM} \
-o ${ALIGN_PATH}/${i}_${SPECIES}_hisat2.bam \
${ALIGN_PATH}/${i}_${SPECIES}_hisat2.sam
${SAMTOOL_PATH}/samtools index ${ALIGN_PATH}/${i}_${SPECIES}_hisat2.bam
${RM_PATH} ${ALIGN_PATH}/${i}_${SPECIES}_hisat2.sam
echo "====================================="
done
##~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~