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