Data resources
|
| Sample Fastq files |
https://bcm.box.com/s/c9q7otvxoog7cmn1b4p9mp8c7thu7q32 |
| Bowtie2 index |
https://ccb.jhu.edu/software/tophat/igenomes.shtml |
|
Protocol 1: DIFFERENTIAL GENE EXPRESSION ANALYSIS OF RNA-SEQ
|
| FastQC |
http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ |
| Tophat2 (Kim, Pertea et al. 2013) |
https://ccb.jhu.edu/software/tophat/index.shtml |
| Samtools (Li, Handsaker et al |
http://www.htslib.org |
| HTSeq (Anders, Pyl et al. 2015) |
https://pypi.python.org/pypi/HTSeq |
| Rstudio |
https://www.rstudio.com/ |
| DESeq2 (Love, Huber et al. 2014) |
http://bioconductor.org/packages/release/bioc/html/DESeq2.html |
| pheatmap |
https://cran.r-project.org/web/packages/pheatmap/ |
|
Protocol 2: DIFFERENTIAL EXPRESSION AND USAGE OF ISOFORMS
|
| Kallisto (Bray, Pimentel et al. 2016) |
https://pachterlab.github.io/kallisto/ |
| Sleuth |
http://pachterlab.github.io/sleuth/about |
| IUTA (Niu, Huang et al. 2014) |
https://ccb.jhu.edu/software/tophat/index.shtml |
| Genome files /GTF files |
http://www.ensembl.org/info/data/ftp/index.html |
|
Protocol 3: CRYPTIC SPLICING
|
| CrypSplice (Tan, Yalamanchili et al. 2016) |
http://www.liuzlab.org/CrypSplice/ |
| IGV (Thorvaldsdottir, Robinson et al. 2013) |
https://software.broadinstitute.org/software/igv/download |
| Bedtools (Quinlan and Hall 2010) |
http://bedtools.readthedocs.io/en/latest/ |
| R: Ibb (Pham, Piersma et al. 2010) |
http://www.oncoproteomics.nl/software/BetaBinomial.html |
| R: MASS |
https://cran.r-project.org/web/packages/MASS/index.html |
