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stat:rnaseq [2023/06/26 14:55] – [2 Alignment] 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:// | ||
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>>GTF [[https:// | >>GTF [[https:// | ||
>>GFF [[https:// | >>GFF [[https:// | ||
+ | |||
+ | ===Alignment Indexing=== | ||
+ | [[https:// | ||
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* STAR | * STAR | ||
* HISAT2 | * HISAT2 | ||
+ | * Salmon [[https:// | ||
===HISAT2=== | ===HISAT2=== | ||
[[https:// | [[https:// | ||
+ | | ||
- | ===Alignment Indexing=== | + | < |
- | [[https://registry.opendata.aws/jhu-indexes/]] | + | 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 | ||
+ | |||
+ | </code> | ||
===STAR=== | ===STAR=== | ||
行 66: | 行 75: | ||
</ | </ | ||
+ | === kallisto | ||
+ | < | ||
+ | # bat | ||
+ | kallisto bus [arguments] FASTQ-files | ||
+ | |||
+ | kallisto quant -i rattus_index_ki/ | ||
+ | |||
+ | </ | ||
====3 Count ==== | ====3 Count ==== | ||
> | > | ||
>>1 [[https:// | >>1 [[https:// | ||
>>> | >>> | ||
+ | < | ||
+ | featureCounts -p -M -O -T 32 -a gtf/ | ||
+ | </ |