stat:rnaseq

差别

这里会显示出您选择的修订版和当前版本之间的差别。

到此差别页面的链接

--- stat:rnaseq [2023/06/25 00:02] – [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
   * RNA-seq 保姆教程：差异表达分析（一） https://zhuanlan.zhihu.com/p/585176027
   * RNA-seq：转录组数据分析处理(上) https://zhuanlan.zhihu.com/p/61847802
+  * Common File Formats Used by the ENCODE Consortium [[https://www.encodeproject.org/help/file-formats/]]
+  * FAA RNA Seq Compare [[https://www.faa.gov/sites/faa.gov/files/GEN_21001B_diffExp_TechReport.pdf]]
-====流程====
+=====流程=====
+[[https://bioconductor.org/packages/release/BiocViews.html#___GeneExpressionWorkflow]]\\
 Raw Data: Fastq (.gz) ->
   - QC: FastQC
@@ 行 16: / 行 20: @@
   - Differential
+====1 QC ====
 ===FastQC===
 <code>
@@ 行 22: / 行 27: @@
 fastqc --noextract RawData/I409/I409_1.fq.gz -o results/1_initial_qc/
 </code>
+====2 Alignment====
 ===基因组注释数据===
@@ 行 31: / 行 39: @@
 >>GFF [[https://ftp.ensembl.org/pub/release-109/gff3/rattus_norvegicus/]]
+===Alignment Indexing===
+[[https://registry.opendata.aws/jhu-indexes/]]
+===对齐工具===
+  * [[https://github.com/pachterlab/kallisto]]
+  * STAR
+  * HISAT2
+  * Salmon [[https://combine-lab.github.io/salmon/getting_started/]]
+===HISAT2===
+[[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 36: / 行 63: @@
   * Github:[[https://github.com/alexdobin/STAR]]
   * Ubuntu Package:[[https://ubuntu.pkgs.org/22.04/ubuntu-universe-arm64/rna-star_2.7.10a+dfsg-1_arm64.deb.html]]
-<code>
+<code bash>
 apt install rna-star
@@ 行 45: / 行 72: @@
 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
+</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.1687651353.txt.gz · 最后更改: 2023/06/25 00:02 由 inkit