能看到这个网站真的是一个意外，现在看来，还是外国人比较认真呀， 这份软件清单，能看出作者的确是花了大力气的，满满的都是诚意。from: https://en.wiki2.org/wiki/List_of_RNA-Seq_bioinformatics_tools
https://en.wiki2.org/wiki/List_of_RNA-Seq_bioinformatics_tools软件主要涵盖了转录组分析的以下18个方向，看我我才明白自己的水平的确没到家，印象中的转录组分析也就是差异表达，然后注释以下，最多分析一下融合基因，要不然就看看那些miRNA，和lncRNA咯，没想到里面的学问也大着呢，怪不得生物是一个大坑，来再多的学者也不怕，咱有的是研究方向给你。
1 Quality control and pre-processing data
1.1 Quality control and filtering data
1.2 Detection of chimeric reads
1.3 Errors Correction
1.4 Pre-processing data
2 Alignment Tools
2.1 Short (Unspliced) aligners
2.2 Spliced aligners
2.2.1 Aligners based on known splice junctions (annotation-guided aligners)
2.2.2 De novo Splice Aligners
2.2.2.1 De novo Splice Aligners that also use annotation optionally
2.2.2.2 Other Spliced Aligners
3 Normalization, Quantitative analysis and Differential Expression
3.1 Multi-tool solutions
4 Workbench (analysis pipeline / integrated solutions)
4.1 Commercial Solutions
4.2 Open (free) Source Solutions
5 Alternative Splicing Analysis
5.1 General Tools
5.2 Intron Retention Analysis
6 Bias Correction
7 Fusion genes/chimeras/translocation finders/structural variations
8 Copy Number Variation identification
9 RNA-Seq simulators
10 Transcriptome assemblers
10.1 Genome-Guided assemblers
10.2 Genome-Independent (de novo) assemblers
10.2.1 Assembly evaluation tools
11 Co-expression networks
12 miRNA prediction
13 Visualization tools
14 Functional, Network & Pathway Analysis Tools
15 Further annotation tools for RNA-Seq data
16 RNA-Seq Databases
17 Webinars and Presentations
18 References