mkdir 00_rawdata #原始序列文件
mkdir 01_trim #储存序列质控后的原始序列文件
mkdir 02_rmhuman #比对到人类基因组上去除人类序列
mkdir 03_metaphlan2 #metaphlan2物种丰度注释文件
mkdir 03_bowtie2 #metaphlan2的中间输出文件
mkdir 04_humann2 #humann2功能注释结果文件
mkdir 04_combined #存放中间文件
mkdir 03_SAM #与ICG gene catalog比对得到的SAM比对结果文件
mkdir 04_genecount #对SAM结果文件进行统计得到的每一个样本的基因计数
mkdir 05_geneprofile # normalized后结果
- Bowtie2
- Trimmomatic
- BWA
- bedtools
- Samtools
- metaphlan2
- humann2
- Human Genome database: /home1/Laisenying/Tools/data/human/hg38
- ICG gene catalog: /home1/Laisenying/.local/share/ngless/data/Modules/igc.ngm/0.9/igc.fna
- chorophlan database: /share/home1/Laisenying/Tools/data/humann2/chocophlan
- uniref database: /share/home1/Laisenying/Tools/data/humann2/uniref
1、------ 原始序列质量控制，并去除宿主(人类)序列 ------
./preprocess.sh accs_id.txt
accs_id.txt : 存放NCBI run_id 的txt文件
- ------ generate species profile -------------
./SpeciesProfile.sh accs_id.txt
- ----- generate functional profile ----------
./FunctionalProfile.sh accs_id.txt
- ----- generate Gene profile ------
python bowtie2_mapping.py \
-s /home1/Laisenying/Data-analysis/CRC/02_rmhuman \
-ref /home1/Laisenying/.local/share/ngless/data/Modules/igc.ngm/0.9/igc.fna \
-o /home1/Laisenying/Data-analysis/CRC/03_SAM \
-BWA /home1/Laisenying/Tools/bwa \
-sam /home1/Laisenying/Tools/samtools/samtools-1.9 \
-bed /home1/Laisenying/Tools/bedtools2-2.25.0/bin \
-list /home1/Laisenying/Data-analysis/CRC/accs_id2.txt
# 合并结果文件
python /home1/Laisenying/Tools/gene_annotation/generate_matrix.py \
-i /home1/Laisenying/Data-analysis/CRC/03_SAM \
-o /home1/Laisenying/Data-analysis/CRC/04_genecount
# TPM normalization and filtered
python /home1/Laisenying/Tools/gene_annotation/normalization.py \
-i /home1/Laisenying/Data-analysis/CRC/04_genecount/DNA_hGEM.txt \
-minTPM 1.0 \
-minSam 1 \
-ref /home1/Laisenying/.local/share/ngless/data/Modules/igc.ngm/0.9/igc.fna \
-o /home1/Laisenying/Data-analysis/CRC/05_geneprofil
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