swh:1:snp:fafdc4d55567af0f04b069bd7bca576c0cea9371
Tip revision: c20430824c5a603eec695ee167e32e4cd1b6c024 authored by Aria on 20 December 2020, 07:48:44 UTC
Update README.md
Update README.md
Tip revision: c204308
10x_scRNA.sh
#!/bin/bash
rawdata1=../../rawdata/scRNA_seq_2020_11_1
rawdata2=../../rawdata/scRNA_seq_2020_11_7
reference=../../rawdata/reference/HeLa_s1_32_and_mm10
result1=../../result/scRNA_seq_2020_11_1
result2=../../result/scRNA_seq_2020_11_7
cellranger=/work/bio-chenr/software/cellranger-3.1.0/cellranger
primary_analysis_1()
{
echo "process will start at:"
date
${cellranger} count --id=${1} \
--transcriptome=${reference} \
--fastqs=${rawdata1}/${1} \
--expect-cells=13000 \
--nosecondary \
--r1-length=28 \
--jobmode=local --localcores=40 --localmem=150
echo "process end at:"
date
}
primary_analysis_2()
{
echo "process will start at:"
date
${cellranger} count --id=${1} \
--transcriptome=${reference} \
--fastqs=${rawdata2}/${1} \
--expect-cells=13000 \
--nosecondary \
--jobmode=local --localcores=40 --localmem=150
echo "process end at:"
date
}
# process technology repeat 1
for prefix in A1A2 C1C2 B1A3; do
{
primary_analysis_1 "${prefix}" > "${result1}/${prefix}.primary_analysis.log" 2>&1
} & done
# process technology repeat 2
for prefix in A1A2 C1C2 B1A3; do
{
primary_analysis_2 "${prefix}" > "${result2}/${prefix}.primary_analysis.log" 2>&1
} & done