[Seqan-dev] Fwd: Re: bug ?!

[Laurent MANCHON <lmanchon@univ-montp2.fr>]

--Hi,

is anyone able to fix the bug in the FAR software developed by Matthias 
Dodt FAR?

thank you --



Hi Laurent!

Sorry for the delay in reply. Yes you are right, there is a bug in the
software. Unfortunately i cannot fix this at the moment since i have
moved out of sience several month ago. I contacted my group but
currently there seems to be nobody taking care of this. I think it
will be fixed in the future, but i can't tell you when. I will get
back to you if i have further information.

thanks,

mat

2012/1/6 laurent manchon<lmanchon@users.sourceforge.net>:
>  --hello,
>
>  i have some problem to clean my sequences using this adaptor string:
>  AATCTCGTATGCCGTCTTCTGCTTGC
>
>  this is my input file:
> > sequence_100104
>  ATAGTCAACGGCTGAGGATTTGGCATCTCGTA
> > sequence_100105
>  ATAGTCAAGATAGAGCTACTGGAGAATCTCGA
> > sequence_100106
>  ATAGTCAAGATAGAGCTACTGGAGAATCTCGT
> > sequence_100107
>  ATAGTCAAGATAGAGCTACTGGGGAATCTCGT
>
>
>  i use this command to clean:
>
>  far --source reads.fa --target reads_no_adapters.fa --adapters myAdapters.fa --format
>  fasta --cut-off 4 --min-overlap 2 --min-readlength 16 --trim-end right
>
>  and this is the output:
>
> > sequence_100104
>  ATAGTCAACGGCTGAGGATTTGGCATCTCGTA
> > sequence_100105
>  ATAGTCAAGATAGAGCTACTGGAGAATCTCGA
> > sequence_100106
>  ATAGTCAAGATAGAGCTACTGGAG
> > sequence_100107
>  ATAGTCAAGATAGAGCTACTGGGG
>
>
>  So, sequence_100106 and sequence_100107 are well cleaned but not
>  sequence_100104, the good results should be:
>
> > sequence_100104
>  ATAGTCAACGGCTGAGGATTTGGC
> > sequence_100105
>  ATAGTCAAGATAGAGCTACTGGAGAATCTCGA
> > sequence_100106
>  ATAGTCAAGATAGAGCTACTGGAG
> > sequence_100107
>  ATAGTCAAGATAGAGCTACTGGGG
>
>  substring \"ATCTCGTA\" is a part of adaptor sequence !
>
>  Somebody has a solution to resolve this problem ?
>
>  thank you.
>
>
>
>
>
>
>
>  --
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