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002_gtf2qnt.sh
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#!/bin/bash
#SBATCH --job-name=qnt_old
#SBATCH --ntasks=64
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=64
#SBATCH --output=%x_%j.log
#SBATCH --partition=normal
#SBATCH -t 240:00:00
module purge # 清除之前挂载的所有模块，我们可以使用conda进行包管理
OPT_DIR="/master/wang_xian_geng/opt"
source ${OPT_DIR}/miniconda3_new/etc/profile.d/conda.sh
conda activate rnaseq
prj_dir="/cpu1/wang_xian_geng/pdac"
base_dir="${prj_dir}/cl/rnaseq/old_idx"
#### purist
# -l IU
# -i
# -1/-2
# --seqBias
# --gcBias
# --posBias
cnf="${prj_dir}/cnf/purist_pe_125.cnf"
fq_dir="/storage2/pdac/rnaseq/purist/raw_fq"
out_dir="${base_dir}/purist"
idx="/cpu1/wang_xian_geng/share/dt/slm_idx/gentrome"
for i in $(cat $cnf); do
if [ ! -f "${out_dir}/${i}/quant.sf" ]; then
salmon quant -i ${idx} -l IU -1 ${fq_dir}/${i}_1.fq.gz -2 ${fq_dir}/${i}_2.fq.gz -p 64 --validateMappings -o ${out_dir}/${i} --seqBias --gcBias --posBias
else
echo "${i} done"
fi
done
cnf="${prj_dir}/cnf/purist_se_66.cnf"
fq_dir="/storage2/pdac/rnaseq/purist/raw_fq"
out_dir="${base_dir}/purist"
# idx="${prj_dir}/cl/new_ref/cl_6_1_flt"
for i in $(cat $cnf); do
if [ ! -f "${out_dir}/${i}/quant.sf" ]; then
salmon quant -i ${idx} -l U -r ${fq_dir}/${i}.fq.gz -p 64 --validateMappings -o ${out_dir}/${i} --seqBias --gcBias --posBias
else
echo "${i} done"
fi
done
#### ccle
cnf="${prj_dir}/cnf/ccle_41.cnf"
fq_dir="/storage2/ccle/rnaseq/pdac/raw_fq"
out_dir="${base_dir}/ccle"
# idx="${prj_dir}/isoseq/new_ref/pdac_4_2"
for i in $(cat $cnf); do
if [ ! -f "${out_dir}/${i}/quant.sf" ]; then
salmon quant -i ${idx} -l IU -1 ${fq_dir}/${i}_1.fq.gz -2 ${fq_dir}/${i}_2.fq.gz -p 32 --validateMappings -o ${out_dir}/${i} --seqBias --gcBias --posBias
else
echo "${i} done"
fi
done
#### amc
cnf="${prj_dir}/cnf/2022-11-28_amc_106.cnf"
fq_dir="/storage2/pdac/rnaseq/amc/raw_fq"
out_dir="${base_dir}/amc"
# idx="${prj_dir}/isoseq/new_ref/pdac_4_2"
for i in $(cat $cnf); do
if [ ! -f "${out_dir}/${i}/quant.sf" ]; then
salmon quant -i ${idx} -l U -r ${fq_dir}/${i}.fq.gz -p 32 --validateMappings -o ${out_dir}/${i} --seqBias --gcBias --posBias
else
echo "${i} done"
fi
done
#### changhai
cnf="${prj_dir}/cnf/changhai_62.cnf"
fq_dir="/storage2/pdac/rnaseq/changhai/raw_fq"
out_dir="${base_dir}/changhai"
# idx="${prj_dir}/isoseq/new_ref/pdac_4_2"
for i in $(cat $cnf); do
if [ ! -f "${out_dir}/${i}/quant.sf" ]; then
salmon quant -i ${idx} -l IU -1 ${fq_dir}/${i}_1.fq.gz -2 ${fq_dir}/${i}_2.fq.gz -p 64 --validateMappings -o ${out_dir}/${i} --seqBias --gcBias --posBias
else
echo "${i} done"
fi
done