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dana

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##1 Merge Process :

Considering 2 DNA fastq sequences:

  • the first one a "classic" DNA sequence, read left to right
  • the second one a complemented and reversed sequence, read right to left

1-1 Convert the complemented and reversed sequence into the "right" way.

1-2 apply drastic thresold

  • Cut all the characters at the end of the first sequence with a quality score lesser than the threshold.
  • Cut all the characters at the begining of the second sequence with a quality score lesser than the threshold.

1-3 Search the 10 first character of the second sequence into the first sequence

  • Search from the end to the begiging of the first sequence
  • if this 10 characters are found into the first sequence : try to merge the 2 sequences

2 The merge problem :

Notes d'Abigail 11/2/2016 Probleme de merge partiel:

  1. choix du seuil de chevauchement minimal (m nucleotides)
  2. si chevauchement(c) inferieur a m (0<c<m), remplacer les c bases du gauche du read R par des X
  3. si c == 0, mettre 2 N sur la fin du read F et le debut du read R
  4. dans les deux cas, coller les deux bouts

(N et X sont pareils mais comme ca on pourra differencier entre les cas 2 et 3)

Probleme de mismatch dans la partie chevauchement: Comme le F et le R viennent du meme molecule, on devrait pas avoir des differences, donc on cherche les matches exactes. On mettra donc pas un 2eme seuil. On veut jeter la sequence s'il y a des differences dans la partie chevauchee.

Exemple que tu m'as envoye: ACTATAACAGACGTATTCACAGTAGGATTAAATATCTCAAGTGCGCAAGGCGTAGACGTCGGGCG ACTATAACAGACGTATTCACAGTAGGATTAAAGATCGAAAGTGGGAAAGGAGTAG

Dans ce cas la, il faut jeter le sequence et faire un note dans le rapport dont tu m'as parle.

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