Slides: https://docs.google.com/presentation/d/1tZ8Li5e_5HV7fm_WdaqjHw0n141OIlNkDBlCjgdp-4o/edit?usp=sharing
RNASeq alignment: Container 1
- Remove contamination from RNAseq reads
- RNAseq alignment to reference assembly: hisat2, stringtie
- input: fastq, reference fasta, contaminant fasta, config file
- output: BAM files and count files
- Snakemake scripts
- Docker with GitHub (badge integration, build)
- Execute with Singularity
Functional annotation: Container 2 (Step 1)
- Blast and Interproscan for functional annotation
- input: fasta file of transcripts and reference gene models
- output: description and domains for transcripts
- Snakemake scripts
Differential expression: Container 2 (Step 2)
- edgeR and DEseq2 for diff expressioninput: counts and meta data file
- output: DE stats
- R scripts and stitching with knitr
- Perl scripts to integrate the functional annotation
- Assign to known gene models if possible with perl script and merge with functional annotation and DE output reports