From: SePIA: RNA and small RNA sequence processing, integration, and analysis
Module | Component | Software | Reference |
---|---|---|---|
Preprocessing | Adaptor and quality trimming | FastX-Toolkit | hannonlab.cshl.edu/ fastx_toolkit/ |
Trimmomatic | [62] | ||
Trim Galore | www.bioinformatics. babraham.ac.uk/ projects/trim_galore/ | ||
Quality statistics | FastQC a | www.bioinformatics. babraham.ac.uk/ projects/fastqc | |
Read mapping | Align sequences to a reference | BWA | [63] |
Tophat | [64] | ||
Bowtie | [13] | ||
Bowtie2 | [65] | ||
STAR | [7] | ||
Alignment sorting and conversion | SAMtools a | [66] | |
Picard tools a | broadinstitute.github. io/picard | ||
Alignment statistics | RNA-SeQC | [67] | |
RSeQC | [68] | ||
Expression | Mapped reads quantification | HTSeq | [69] |
Cufflinks | [70] | ||
Analysis | Variant calling | Bambino | [35] |
and annotation | ANNOVAR | [71] | |
Differential expression | Cuffdiff | [18] | |
R bioconductor packages for differential expression | DESeq | [15] | |
DESeq2 | [72] | ||
DEXseq | [73] | ||
EdgeR | [14] | ||
novel miRNA discovery | miRanalyzer | [74] | |
miRDeep2 | [75] | ||
miRNA-mRNA integration | R package for SQLite query | sqldf a | [76] |
Pathway impact analysis | SPIA | [77] |