Other applications of RNA-seq A non-comprehensive list - - PowerPoint PPT Presentation
Other applications of RNA-seq A non-comprehensive list Identifying the protein interaction sites on RNA molecules: HITS-CLIP , PAR-CLIP , iCLIP Identifying translation status of genes: Ribo-seq (Ribosomal Profiling)
https://en.wikipedia.org/wiki/CLIP#/media/File:Basic_Principle_of_CLIP.jpg
Sequence reads trimming Alignment to Genome: bowtie, STAR Detect potential binding regions + annotate binding genes collapse reads into unique reads for all samples
FASTQ multiple fastq BAM 1 fastq with unique ids
Identify true binding sites + Statistical analysis Identify mutations Quality control: FASTQC
Nature Reviews Genetics 15, 205–213 (2014) doi:10.1038/nrg3645
Nature Reviews Genetics 15, 205–213 (2014) doi:10.1038/nrg3645
Sequence reads DGE with R: DESeq2, EdgeR, limma:voom
FASTQ FASTQ
Pseudocounts with Kallisto, Sailfish, Salmon
(+reference transcriptome index) Count matrix generated using tximport
Quality control: FASTQC
Sequence reads trimming Alignment to Genome: bowtie, STAR DGE with R: DESeq2, EdgeR, limma:voom Detect clusters over the genome: seqcluster Count reads on known small RNAs: seqbuster, tdrmapper
FASTQ Count Matrix (+known GTF, optional) multiple fastq (+known reference: miRBase, tRNAs …) BAM 1 fastq with unique ids Count Matrix
novel miRNA: miRDeep2
Quality control: FASTQC collapse reads into unique reads for all samples