Manually adjusted primer sets (removed adaptors). This is a backup in case
that primers/ is overwritten.

IGH:
- Xho: ctcgag
IGK:
- Sac1: gagctc

Listing with primer sets with 0 cvg
---------------------------------
IGH
------------
IPS000032_Persson1991: done
IPS000046_Cardona1995: nothing found
IPS000069_Rubinstein1998: removed xho sites.
IPS000095_Glamann1998: done
IPS000221_vanDongen2003: nothing found
Kueppers1993_IGHV_1st: nothing found -> analysis of rearranged genes ->
primers don't bind to 'normal genes'?

IGK:
IPS000038_Persson1991: already done
IPS000045_Atkinson1996: Xho1 sites not contained in all primers?
IPS000049_Chen1986: nothing found
IPS000063_Giachino1995: nothing found (germline cells)
IPS000078_Glamann1998:  already done
IPS000088_Rubinstein1998:  removed sac1 site.
IPS000121_Cox1994: HindIII restriction site removed.
IPS000122_Padyukov2001: HindIII and Xho1 sites removed. Combine IPS000122 and
IPS000126 into one set.
IPS000154_Juul1997: MboI site removed.
IPS000158_Huber1993: not clear which sites are present?
IPS000160_Timmers1993: removed Xba1 sites.
Kueppers1993_IGKV_1st:  already done

IGL:
IPS000073_Stiernholm1994: no access :-(
IPS000083_Moraes2003: added a missing sequence, no adaptors (ecoR1?)
IPS000145_Rubinstein1998: removed sac1 site.
Tiller2008_IGLV_1st: no restriction sites found! primer still don't 'work',
TODO?
Wardemann2003_IGLV_1st: are the same as the Murugan2015 primers and I couldn't
find a corresponding publicatio, so i removed this set ..

Comparison:
- only consider 1st primers of nested PCR!

Listing of primer sets with one primer with 0 cvg:

IGH:
- Brezinschek
ccatggactggacctgg
cacaggccccctaccagc
-> Die primer wuerden ohne "cc" vorne binden! mehr mismatches erlauben? Kein
Zugriff aufs Paper.
- Ippolito
tcaacacaacggttcccagtta
-> VH3N primer (VH3-23)
- vanEs: removed restriction sites from two primers where sites were not
  removed yet.
- Verhagen
>Verhagen2000|IGHV2-10*01|2
aacagtgatcaacatggacattgtg
>Verhagen2000|IGHV3-15*05|4
ctatctgcaaatggacagtctgaaa
-> konnte keine Info ueber restriction finden.
- Lim2010
tcaacacaacggttcccagtta
-> VH3N primer wie bei Ippolito ...

Conclusion: do we miss VH3N in our templates?

IGK:
- Cardona1995
>Cardona1995|IGKV4-1*01|15
gacatcgtgatgacccagttctc
-> Konnte nichts finden.
- Burg2001
van2001|IGKV7-3*01|29	aggacagagggccaccatcacc
-> Konnte nichts finden.
- vanDongen2003
van2003|IGKV|6	gaccgatttcaccctcacaattaatcc
-> nichts gefunden.
- Lim2010
Lim2010|VK2N1|5	agatgctgtgtgamccagcctc
Lim2010|VK2N2|6	tccctccaagttcacatcctgag
-> Both primers are a Design for putative functional genes suggested from VBASE2.
- Murugan2015
Murugan2015|5' L-Vk1/2|1 atgaggstcccygctcagctgctgg
-> Konnte nichts finden
- Tiller2008
Tiller2008|5_L_Vk_1/2|1	atgaggstcccygctcagctgctgg
-> Gleicher primer wie bei Murugan. Hat Murugan 'abgeschrieben von Tiller'?
Tiller sagt auch nichts besonders ueber den primer.
- Wardemann2003
Wardemann2003|5' L V魏1/2|1	atgaggstcccygctcagctgctgg
-> Gleicher wie bei Tiller2008/Murugan2015. Wardemann gibt im Suppl. auch
keine Beschreibung ab.

Conclusion: Should we consider putative functional genes (VBASE2)? What is
wrong with the IGK 1/2 primer?

IGL:
- Ippolito2012
Ippolito2014|VL3-fwd|5	tcctatgwgctgacwcagccaa
-> Nichts gefunden
- Marks1991
Marks1991|IGLV4-69*01|5	cacgttatactgactcaaccgcc
-> konnte nichts finden
- Lim2010
Lim2010|Vl3|5	tcctatgwgctgacwcagccaa
Lim2010|VlNA|10	gtccagttcctctattatgrtag
-> Zweiter primer ist wieder experimentell (putative). Beim ersten primer
reporten sie coverage auch mit 1 mismatch...
- Sblattero1998
Sblattero1998|VL3back|2	tcctatgwgctgacwcagccaa
-> Gleicher primer with Ippo/Lim2010

Conclusion:
Was ist mit dem tcctatgwgctgacwcagccaa Primer los?

Summary
-----------
IGH:
- What about the VH3N primer tcaacacaacggttcccagtta?
IGK:
- What is wrong with the IGK 1/2 primer atgaggstcccygctcagctgctgg?

IGL:
- What is wrong with the VL3 primer tcctatgwgctgacwcagccaa?

General:
- Should we consider putative functional genes (VBASE2)?
