Revision a488b15c0418a8e604ce6339aae7b505ae3252c9 authored by Aria on 20 December 2020, 06:24:49 UTC, committed by GitHub on 20 December 2020, 06:24:49 UTC
1 parent 2919a0c
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
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