https://bioconductor.org/packages/release/BiocViews.html#___GeneExpressionWorkflow
Raw Data: Fastq (.gz) →
apt install fastqc fastqc --noextract RawData/I409/I409_1.fq.gz -o results/1_initial_qc/
https://daehwankimlab.github.io/hisat2/download/ * https://notebook.community/ssjunnebo/pathogen-informatics-training/Notebooks/RNA-Seq/genome-mapping
hisat2-build -p 32 fasta/Rattus_norvegicus.mRatBN7.2.dna.toplevel.fa hisat_index hisat2 -x hisat_index/hisat_index -1 I409/I409_1.fq.gz -2 I409/I409_2.fq.gz -S I409.sam -p 32
2.7.10b
apt install rna-star # 创建索引,索引文件创建一次即可. 需要从Ensembl下载对应物种的Fasta文件和GTF文件。 STAR --runMode genomeGenerate --genomeDir star_index --genomeFastaFiles fasta/* --sjdbGTFfile gtf/* --runThreadN 14 # 运行分析 STAR --genomeDir star_index --readFilesIn filtered/sample_filtered.fq --outSAMtype BAM SortedByCoordinate --quantMode GeneCounts --runThreadN 14 STAR --genomeDir star_index --readFilesIn rna4/RawData/I409/I409_1.fq --outSAMtype BAM SortedByCoordinate --quantMode GeneCounts --runThreadN 14
# bat kallisto bus [arguments] FASTQ-files kallisto quant -i rattus_index_ki/transcriptome.idx -o reads.kallisto_quant -t 64 --fusion --pseudobam --genomebam --gtf gtf\Rattus_norvegicus.mRatBN7.2.109.gtf rna4\RawData\I409\I409_1.fq.gz rna4\RawData\I409\I409_2.fq.gz
featureCounts -p -M -O -T 32 -a gtf/Rattus_norvegicus.mRatBN7.2.109.gtf -o output.txt data.sam [bam]