lncRNA分析跟常见的mRNA-seq分析重合度很高，无非也是把测序的fastq文件mapping到参加基因组，获取转录本信息，转录本表达定量，表达量的差异分析，比较新的分析就是把转录本分成了lncRNA和mRNA，这样可以考虑它们之间的互相作用，也可以在实验设计的时候加入miRNA和CHIP-seq，这样多种数据结合分析，显得更高大上一点，也能更好的刻画机体状态，从而回答生物学假设，我这里先列出我的自学大纲，如果有朋友想跟着我学习，可以发email给我，我的邮箱是jmzeng1314，是163邮箱，发信给我前，先看如果你希望我回答你的问题 这篇文章：
step1:read paper and get the workflow for lncRNA anlaysis
## Integration of Genome-wide Approaches Identifies lncRNAs of Adult Neural Stem Cells and Their Progeny In Vivo
step2:download the raw data from NCBI-GEO-SRA database
step3:quality control for the sequence data
## paper:2012- analysis of RNA-seq experiments with TopHat and Cufflinks : http://www.nature.com/nprot/journal/v7/n3/full/nprot.2012.016.html
## 作者用的是tophat2+cufflinks+CummeRbund 我这里替换成HISAT+StringTie+ballgown
step4:mapping the reads to reference genome/transcriptome
step5: de nove identification lncRNA
paper:Genome-wide computational identification and manual annotation of human long noncoding RNA genes :http://rnajournal.cshlp.org/content/16/8/1478.short
paper:A complete annotation of CaptureSeq-derived transcripts is available at http://neurosurgery.ucsf.edu/danlimlab/lncRNA.
step6:counts the expression lever for each LncRNA
step7:find the differentially expressed LncRNA
step8: function anlaysis for the lncRNA
paper:2016-Discovery and functional analysis of lncRNAs: http://www.sciencedirect.com/science/article/pii/S1874939915002163
paper:2014-Genome-wide screening and functional analysis identify a large number of long noncoding RNAs involved in the sexual reproduction of rice: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-014-0512-1
Introduction: sequence-->expression-->function: http://www.exiqon.com/lncrna
paper:2014-lncRNAtor-a comprehensive resource for functional investigation of long noncoding RNAs:http://lncrnator.ewha.ac.kr/index.htm
paper:2014-Genome-Wide Analysis of Long Noncoding RNA (lncRNA) Expression in Hepatoblastoma Tissues : http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0085599
paper:2015- Predicting the Functions of Long Noncoding RNAs Using RNA-Seq Based on Bayesian Network: http://www.hindawi.com/journals/bmri/2015/839590/
paper:2016-Long Non-coding RNA in Neurons: New Players in Early Response to BDNF Stimulation : http://journal.frontiersin.org/article/10.3389/fnmol.2016.00015/full
Figure 7: GO analysis of the biological function of lncRNA: http://www.nature.com/articles/srep21499/figures/7
Figure 2. GO enrichment analysis of lncRNA targets. GO annotations of lncRNA targets categorized by (A) biological process, (B) cell component and (C) molecular function. :https://www.spandidos-publications.com/or/31/4/1613 ## http://www.oatext.com/Genome-wide-analysis-of-differentially-expressed-long-noncoding-RNAs-induced-by-low-shear-stress-in-human-umbilical-vein-endothelial-cells.php
Figure 3. Functional classification of lncRNA : https://www.spandidos-publications.com/ijo/45/2/619
paper:2016-Expression profiles of long-noncoding RNAs in cutaneous squamous cell carcinoma. : http://www.futuremedicine.com/doi/abs/10.2217/epi-2015-0012
step9:lncRNA-mRNA co-expression network
paper:2015-biomarkers-OV-Comprehensive analysis of lncRNA-mRNA co-expression patterns: http://www.nature.com/articles/srep17683
paper:2016-Differential lncRNA-mRNA co-expression network analysis : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4732855/
paper:2014-Microarray Profiling and Co-Expression Network Analysis of Circulating lncRNAs and mRNAs :http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0093388
paper:2014-Long Noncoding RNA-EBIC Promotes Tumor Cell Invasion by Binding to EZH2 and Repressing E-Cadherin in Cervical Cancer : https://figshare.com/articles/_lncRNA_mRNA_co_expression_network_/1098837
paper:2016-Microarray Analysis of lncRNA and mRNA Expression Profiles in Patients with Neuromyelitis Optica : http://link.springer.com/article/10.1007/s12035-016-9754-0
paper:2015-LncRNA expression profiles reveal the co-expression network in human colorectal carcinoma : http://www.ijcep.com/files/ijcep0017983.pdf
step10: analysis of lncRNA-miRNA interactions
paper:2014-starBase-decoding miRNA-ceRNA, miRNA-ncRNA and protein–RNA interaction networks from large-scale CLIP-Seq data : http://nar.oxfordjournals.org/content/early/2013/11/30/nar.gkt1248.short
paper:2014-An Integrated Analysis of miRNA, lncRNA, and mRNA Expression Profiles : http://www.hindawi.com/journals/bmri/2014/345605/abs/
paper:2013-Systematic transcriptome wide analysis of lncRNA-miRNA interactions : http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0053823
Figure: Regulatory cancer network of lncRNA-miRNA interactions. : http://www.aimspress.com/article/10.3934/molsci.2016.2.104/fulltext.html
paper:2014-Functional interactions among microRNAs and long noncoding RNAs :http://www.sciencedirect.com/science/article/pii/S1084952114001700
paper:2014-NPInter v2.0-an updated database of ncRNA interactions: http://nar.oxfordjournals.org/content/42/D1/D104.short
paper:2013-Long Noncoding RNAs-Related Diseases, Cancers, and Drugs: http://www.hindawi.com/journals/tswj/2013/943539/abs/
step11: Histone Modifications and lncRNA Expression
paper:2013-Panning for Long Noncoding RNAs : http://www.mdpi.com/2218-273X/3/1/226/htm
2015-Analysis of long non-coding RNAs highlights tissue-specific expression patterns and epigenetic profiles in normal and psoriatic skin : https://genomebiology.biomedcentral.com/articles/10.1186/s13059-014-0570-4
2013-Predicting long non-coding RNAs using RNA sequencing : http://www.ncbi.nlm.nih.gov/pubmed/23541739
2014-Identification of prostate cancer LncRNAs by RNA-Seq ： http://www.ncbi.nlm.nih.gov/pubmed/25422238
book: Identification of Disease-Related Genes by NGS: http://www.diss.fu-berlin.de/diss/servlets/MCRFileNodeServlet/FUDISS_derivate_000000015470/Dorn_Cornelia.diss2.pdf
book: yeast function genomic : http://download.springer.com/static/pdf/150/bok%253A978-1-4939-3079-1.pdf?originUrl=http%3A%2F%2Flink.springer.com%2Fbook%2F10.1007%2F978-1-4939-3079-1&token2=exp=1467776101~acl=%2Fstatic%2Fpdf%2F150%2Fbok%25253A978-1-4939-3079-1.pdf%3ForiginUrl%3Dhttp%253A%252F%252Flink.springer.com%252Fbook%252F10.1007%252F978-1-4939-3079-1*~hmac=4aaa3f402c498fffa9c609d6ab14c14c0eba3b7862a526ecfddf30c0cf7fb81f
RNA-seq workflow tophat+cufflinks+R: https://s3-eu-west-1.amazonaws.com/pfigshare-u-files/1100005/20130522GACDRNASeqandMethylation.pdf
mRNA and ncRNA (miRNA, lncRNA, snoRNA, etc)
Quantitative gene profiling of long noncoding RNAs with targeted RNA sequencing : http://www.nature.com/nmeth/journal/v12/n4/full/nmeth.3321.html
Targeted RNA sequencing reveals the deep complexity of the human transcriptome http://cole-trapnell-lab.github.io/pdfs/papers/mercer-capture-seq.pdf
Targeted sequencing for gene discovery and quantification using RNA CaptureSeq http://www.ncbi.nlm.nih.gov/pubmed/24705597
2011年 RNA CaptureSeq技术出现 ： http://www.ebiotrade.com/newsf/2011-11/20111117145845614.htm