Introduction | How ORFik organizes stored files | Specify output folders | Download RNA-seq NGS data | Annotation (Fasta genome and gtf file) | Download genome and gtf files | Contaminants | Local annotation | Annotation without defined UTRs | Create 5' UTR annotation from CAGE | Create Pseudo 5' UTR annotation | Fixing malformed gtf/gff | RNA-seq alignment | Indexing | Trimming and Aligning the data | Trimming data | Aligning the data | UMIs | Collapsing duplicated reads | Solving errors when aligning: | RAM usage warnings | Systems that restricts max open files | Restart STAR from crashed step | Create an ORFik experiment of the Yeast data | Post alignment QC report | Convert libraries to new formats | Outputting libraries to R | FPKM values (normalized counts) | Session information

Introduction | Motivation | What is an ORFik experiment? | creating an ORFik experiment | A minimal experiment | Fixing or updating an experiment | ORFik example experiment | The experiment object | Accessing library file paths | Loading data from experiment | Loading NGS data to environment | Loading NGS data as list | Loading NGS data by fimport | Loading Annotation and specific regions | Plotting with ORFik experiments | P-site shifting experiment | Converting bam files to faster formats | ofst: ORFik serialized format | bedo: bed ORFik file (to be deprecated!) | bedoc: bed ORFik file with cigar (to be deprecated!) | ORFik QC report | General report | How to run QC: | How to load optimized output from QC: | How to load the QC statistics: | How to see the QC plots: | Ribo-seq specific pshifting and QC | Using the ORFik experiment system in your script | Note for windows users | Looping over all libraries in experiment | Reformat output to data.table (merge column-wise) | Reformat output to data.table (merge row-wise) | Conclusion | Session information

Introduction | Motivation | Importing Sequencing reads | Loading files (general) | Bam files | Other formats | Exporting to new formats | Files are not preload into R | BAM to OFST (keep cigar information) | BAM to bigwig (do not keep cigar information or read lengths) | Files are preload into R | Random access | Importing Annotation | Loading Genome index (fasta index) | Loading Gene annotation (Txdb) | Loading Transcript regions | Loading Transcript regions (filtering) | Loading Transcript regions (filtering by length requirements) | Loading Transcript regions (filtering by canonical isoform) | Loading uORF annotation | Session information

Introduction | Finding Open Reading Frames | Example of finding ORFs in on 5' UTR of hg19 | Saving coordinates of ORFs to disc | Getting sequences from ORFs | Getting DNA fasta sequences of ORFs | Amino acid sequences of ORFs | New GRanges and GRangesList utilities for ORFs | Grouping ORFs | Filtering example | ORF interest regions | When to use which ORF-finding function | Finding ORFs in spliced transcripts | Prokaryote/Circular Genomes and fasta transcriptomes. | Filter on strand | CAGE data for 5' UTR re-annotation | RiboSeq footprints automatic shift detection and shifting | Gene identity functions for ORFs or genes | Calculating Kozak sequence score for ORFs | Using ORFik in your package or scripts | Coverage plots made easy with ORFik | Multiple data sets in one plot | Conclusion | Session information

Introduction | Pipeline | Session information

Introduction | Pipeline

Introduction | Motivation | Getting data | Loading Transcript region (single point locations) | Loading Transcript region (window locations) | Extending transcript into genomic flanks | Coverage over transcript regions | Loading NGS data | Total counts per region/window | Per nucleotide in region/window | Per nucleotide in region/window (split by read length) | Advanced details | Session information