HLA typing: TODOs

[shiltemann]

• Workflow changes

  • [x] Sample name as workflow parameter for better output dataset naming
  • [x] PEAR
  • [x] give percentage along with count
  • [x] adapter clipping (Cutadapt)
  • [ ] disease association (compare to small list ~8 associated types)
  • [x] take reverse complement of reverse reads before paste step (done by PEAR
  • [x] Add BLAST+ links/results
  • [ ] collection-enable paste step (paste pairs together side by side for each pair in collection)

• Create output report

  • [x] barplot
  • [ ] table with 4 fields per patient: bin1/bin2 vs A/B side of gene
  • [ ] disease association

• QC

  • [ ] QC: check that two different files were given for forward and reverse reads
  • [ ] QC: size of 3rd bin in het or size of second bin in hom call: flag if over threshold

Future

• [ ] they will sequence exon3 as well (currently just exon2)

[shiltemann]

From Elana regarding primer trimming:

Deze sequenties moeten van de uitslagen afgehaald worden:

F: CTTG TCATCTTCAC TCATCAG
R: CATACCATTGGTAGCAG 

De R is reversed complementair, dus wellicht handig om de reversed sequenties ook meteen complementair te maken! Lukt dat zo? Of moet ik een voorbeeldje geven? Groetjes,Elana