Aim = Analysis of nanopore (canine) (transcriptomic) data
Methods
-
Manopore :
- aim : QC and processing of nanopore reads
- method :
- nextflow
- pipeline with different tools
- results :
- QC : nanocomp plots on DCS109, Number of reads, median length
- QC: mapping with minimaps (% reads mapped, unmapped...)
- from Workman et al.: "The 360,000 unaligned pass reads had a median read length of 211 bases."
- QC : guppy versions impact on QC
-
MacFab :
- aim : 4 tools to reconstruct transcipt isoforms from nanopore
- mehod :
- snakemake
- short description of the 4 methods
- results
- Descriptive statistics
- per sample SQANTI
- comparing samples with SQUANTI-like output.
- merging all fastq
- nb of isoforms /genes
- knonwn vs novel isoforms/genes
- number of 5' vs 3' extensions vs
- RGASP-like comparison from macFab
- saturated plotversu num reads
- at the gn and tx levels
- lncRNAs vs mRNA reconstruction : RSEQC prelim analysis
- lncRNAs may have specific pattern RT switching or splicing miasannotation as it is not reported in RNADirect run.
- Descriptive statistics
Ccl/perspectives/ToDo list
- Manopore:
- add new guppy versions (
bonito
)
- add new guppy versions (
- MacFab
- new macfab methods ?
- Transcript validation (TTS = CAGE ; TSS = tailFinder)
Notes:
- Focus on transcriptome reconstruction rather than quantification (no SIRVs)
- Focus on lncRNAs reconstruction
- Check talon vs bambu same number of isoforms
- Check ORF annotation from SQANTI