stat:rnaseq

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--- stat:rnaseq [2023/06/26 14:34] – [流程] inkit
+++ stat:rnaseq [2024/04/04 23:32] (当前版本) – [教程] inkit
@@ 行 1: / 行 1: @@
 ====== RNA-Seq ======
 ====教程====
+  * 向SRA提交数据 [[stat:rnaseq:srasubmit]]
   * 知乎搜索 https://www.zhihu.com/search?q=rnaseq%20fastq%20star&type=content
   * RNA-Seq数据标准化方法 https://zhuanlan.zhihu.com/p/37196518
@@ 行 37: / 行 38: @@
 >>GTF [[https://ftp.ensembl.org/pub/release-109/gtf/rattus_norvegicus/]]
 >>GFF [[https://ftp.ensembl.org/pub/release-109/gff3/rattus_norvegicus/]]
+===Alignment Indexing===
+[[https://registry.opendata.aws/jhu-indexes/]]
@@ 行 42: / 行 46: @@
   * [[https://github.com/pachterlab/kallisto]]
   * STAR
+  * HISAT2
+  * Salmon [[https://combine-lab.github.io/salmon/getting_started/]]
-===Alignment Indexing===
+===HISAT2===
-[[https://registry.opendata.aws/jhu-indexes/]]
+[[https://daehwankimlab.github.io/hisat2/download/]]
+ *  [[https://notebook.community/ssjunnebo/pathogen-informatics-training/Notebooks/RNA-Seq/genome-mapping]]
+<code>
+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
+</code>
 ===STAR===
@@ 行 62: / 行 75: @@
 </code>
+=== kallisto  ===
+<code>
+# 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
+</code>
 ====3 Count ====
 >可以Reads的工具[[https://hbctraining.github.io/Intro-to-rnaseq-hpc-O2/lessons/05_counting_reads.html]]
 >>1 [[https://subread.sourceforge.net/]]
 >>>featureCounts [[https://rnnh.github.io/bioinfo-notebook/docs/featureCounts.html]]
+<code>
+featureCounts -p -M -O -T 32 -a gtf/Rattus_norvegicus.mRatBN7.2.109.gtf -o output.txt data.sam [bam]
+</code>

stat/rnaseq.1687790049.txt.gz · 最后更改: 2023/06/26 14:34 由 inkit