Question: Alignment to reference containing ambiguity code
gravatar for Karol Pal jr.
6.3 years ago by
Czech Republic
Karol Pal jr.20 wrote:


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

ADD COMMENTlink modified 3.1 years ago by otetelis0 • written 6.3 years ago by Karol Pal jr.20

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

ADD REPLYlink modified 6.3 years ago • written 6.3 years ago by Ashutosh Pandey12k

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

ADD REPLYlink modified 6.3 years ago • written 6.3 years ago by Karol Pal jr.20
gravatar for otetelis
3.1 years ago by
otetelis0 wrote:

Hi Karol,

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

Best regards, Joana

ADD COMMENTlink written 3.1 years ago by otetelis0

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

ADD REPLYlink written 3.1 years ago by Karol Pal jr.20

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

ADD REPLYlink written 6 months ago by mschmidt50
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