Alignment to reference containing ambiguity code

Question

[Karol Pal jr.]

Hi,

I am trying to align reads to a reference, which contains ambiguity code. Mosaik claims to be able to do this but somehow fails... All the reads were generated from the reference sequence but do not contain ambiguity code ( e.g. if there is an M in the reference the read has either an A or a C). Does anyone have any experience with this?

Thanks in advance

[Ashutosh Pandey]

Are you sure that the failing has to do something with the ambiguous bases. Can you post the "error" ?

[Karol Pal jr.]

Thank you for the fast reply... No I'm not sure, this is the alignment statistics I get:

managed to align SOME reads with a different version (latest, precompiled, unix) still many filtered out for unknown reason

Alignment statistics (mates):
================================================
   # failed hash:               398896 (  7.6 %)
------------------------------------------------
# unaligned mates(X):           398896 (  7.6 %)
# filtered out(F):             4833106 ( 92.4 %)
================================================
total aligned:                       0 (  0.0 %)
total:                         5232002

Alignment statistics (pairs):
===================================================================
                                  Local rescues   Frag. consistency

Both ends unaliged pairs
-------------------------------------------------------------------
# F-F pairs:    2301569 ( 88.0 %)
# F-X pairs:     229968 (  8.8 %)
# X-X pairs:      84464 (  3.2 %)
===================================================================
total aligned:        0 (  0.0 %)             0                   0

[otetelis]

Hi Karol,

have you found a solution for your problem? I have the same issue.

Best regards,
Joana

[Karol Pal jr.]

I'm sorry to disappoint you, I have never truly solved this problem. If anything I try to avoid ambiguity code after this experience :) .

[mschmidt]

Hi Joana, I am looking for similar solution. You are over 2 yrs ahead with that problem. Did you solved it? Can you help?

Kind regards,
Marcin