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stat:rnaseq [2023/06/26 00:29] – [教程] inkit | stat:rnaseq [2024/04/04 23:32] (当前版本) – [教程] inkit | ||
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====== RNA-Seq ====== | ====== RNA-Seq ====== | ||
====教程==== | ====教程==== | ||
+ | * 向SRA提交数据 [[stat: | ||
* 知乎搜索 https:// | * 知乎搜索 https:// | ||
* RNA-Seq数据标准化方法 https:// | * RNA-Seq数据标准化方法 https:// | ||
行 8: | 行 9: | ||
* FAA RNA Seq Compare [[https:// | * FAA RNA Seq Compare [[https:// | ||
- | ====流程==== | + | =====流程===== |
+ | [[https:// | ||
Raw Data: Fastq (.gz) -> | Raw Data: Fastq (.gz) -> | ||
- QC: FastQC | - QC: FastQC | ||
行 18: | 行 20: | ||
- Differential | - Differential | ||
+ | ====1 QC ==== | ||
===FastQC=== | ===FastQC=== | ||
< | < | ||
行 24: | 行 27: | ||
fastqc --noextract RawData/ | fastqc --noextract RawData/ | ||
</ | </ | ||
+ | |||
+ | |||
+ | ====2 Alignment==== | ||
===基因组注释数据=== | ===基因组注释数据=== | ||
行 32: | 行 38: | ||
>>GTF [[https:// | >>GTF [[https:// | ||
>>GFF [[https:// | >>GFF [[https:// | ||
+ | |||
+ | ===Alignment Indexing=== | ||
+ | [[https:// | ||
行 37: | 行 46: | ||
* [[https:// | * [[https:// | ||
* STAR | * STAR | ||
+ | * HISAT2 | ||
+ | * Salmon [[https:// | ||
+ | |||
+ | ===HISAT2=== | ||
+ | [[https:// | ||
+ | | ||
+ | |||
+ | < | ||
+ | hisat2-build -p 32 fasta/ | ||
+ | hisat2 -x hisat_index/ | ||
+ | |||
+ | </ | ||
===STAR=== | ===STAR=== | ||
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STAR --genomeDir star_index --readFilesIn rna4/ | STAR --genomeDir star_index --readFilesIn rna4/ | ||
+ | </ | ||
+ | |||
+ | === kallisto | ||
+ | < | ||
+ | # bat | ||
+ | kallisto bus [arguments] FASTQ-files | ||
+ | |||
+ | kallisto quant -i rattus_index_ki/ | ||
+ | |||
+ | </ | ||
+ | ====3 Count ==== | ||
+ | > | ||
+ | >>1 [[https:// | ||
+ | >>> | ||
+ | < | ||
+ | featureCounts -p -M -O -T 32 -a gtf/ | ||
</ | </ |