Resources
Reference Genomes¶
| Name | Species | Common name | Annotation Version |
|---|---|---|---|
| hg38 | Homo sapiens | Human | Genome Reference Consortium Human Build 38 |
| mm10 | Mus musculus | House mouse | Genome Reference Consortium Mouse Build 38 |
Software¶
Quality control and pre-processing¶
| Package/Tool | Version | Usage | Reference |
|---|---|---|---|
| FastQC | 0.11.5 | Preliminary quality control on FASTQ reads before and after adapter trimming | 1 |
| Cutadapt | 1.18 | Adapter sequence trimming | 2 |
| Kraken | 1.1 | Assesses microbial contamination | 3 |
| KronaTools | 2.7 | Visualizes results from Kraken | 4 |
| FastQ Screen | 0.9.3 | Assesses sequence contamination | 5 |
| MultiQC | 1.4 | QC report aggregation and generation | 6 |
| FASTX-Toolkit | 0.0.14 | FASTA and FASTQ conversion kit | 7 |
Alignment and differential expression¶
| Package/Tool | Version | Usage | Reference |
|---|---|---|---|
| miRDeep2 | 2.0.0.8 | Backbone for miRSeq alignment and quantification. Dependencies include Bowtie1, ViennaRNA, RandFold, and Perl | 8, 9, 10, 11, 12 |
| edgeR | 3.28.1 | Normalization and differential miR expression analysis | 13, 14 |
| R | 3.6.1 | Programming language used to run edgeR | 15 |
References¶
1 Andrews, S. 2018. "FastQC: A quality control tool for high throughput sequence data." http://www.bioinformatics.babraham.ac.uk/projects/fastqc/. Version 0.11.5
2 Martin, M. 2011. "Cutadapt removes adapter sequences from high-throughput sequencing reads." EMBnet.journal 17(1): 10-12. doi: 10.14806/ej.17.1.200
3 Wood and Salzberg. 2014. "Kraken: ultrafast metagenomic sequence classification using exact alignments." Genome Biol. 15: R46. doi: 10.1186/gb-2014-15-3-r46
4 Ondov, Bergman, and Phillippy. 2011. "Interactive metagenomic visualization in a Web browser." BMC Bioinformatics 12: 385. doi: 10.1186/1471-2105-12-385
5 Wingett and Andrews. 2018. "FastQ Screen: A tool for multi-genome mapping and quality control." F1000Res. 7: 1338. doi: 10.12688/f1000research.15931.2
6 Ewels, Magnusson, et al. 2016. "MultiQC: Summarize analysis results for multiple tools and samples in a single report." Bioinformatics 32(19): 3047-3048. doi: 10.1093/bioinformatics/btw354
7 Gordon, A. 2010. "FASTX-Toolkit: FASTQ/A short-reads pre-processing tools." http://hannonlab.cshl.edu/fastx_toolkit/index.html
8 Friedlander, Mackowiak, et al. 2012. "miRDeep2 accurately identifies known and hundreds of novel microRNA genes in seven animal clades." Nucleic Acids Res. 40(1): 37-52. doi: 10.1093/nar/gkr688
9 Langmead, Trapnell, et al. 2009. "Ultrafast and memory-efficient alignment of short DNA sequences to the human genome." Genome Biol. 10: R25. doi: 10.1186/gb-2009-10-3-r25
10 Lorenz, Bernhart, et al. 2011. "ViennaRNA Package 2.0." Algorithms Mol Biol. 6: 26. doi: 10.1186/1748-7188-6-26
11 Bonnet, Wuyts, et al. 2004. "Evidence that microRNA precursors, unlike other non-coding RNAs, have lower folding free energies than random sequences." Bioinformatics 20(17): 2911-2917. doi: 10.1093/bioinformatics/bth374
12 "perl - The Perl 5 language interpreter." 2017. https://www.perl.org. Version 5.24.3.
13 Robinson, McCarthy, and Smyth. 2010. "edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26: 139-140. doi: 10.1093/bioinformatics/btp616
14 McCarthy, Chen, and Smyth. 2012. "Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation." Nucleic Acids Res. 40(10): 4288-4297. doi: 10.1093/nar/gks042
15 "The R Project for Statistical Computing." https://www.r-project.org/. Version 3.6.1, released 2019-07-05.