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cap3 alignment viewer (Read 12831 times)

Aug 19^th, 2011 at 5:58pm

Rob Offline
YaBB Newbies

Posts: 2

When I assembly sequences using cap3 the sequences the assembly viewer does not reverse complement sequences correctly.

I am using UGENE 1.9.5 on windows xp and OsX with similar results

I have created a sequence and assembling it with its reverse complement does not give the correct alignment. I have attached a fasta files and screen shot to demonstrate.

Is this a bug or am I not carrying out the assembly correctly?

1.fa (0 KB | )

2.fa (0 KB | )

screenshot.tiff (36 KB | )

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Reply #1 - Aug 22^nd, 2011 at 4:22pm

Konstantin Okonechnikov Offline
Global Moderator

Posts: 173

Hi Rob,

I've investigated the issue - it's a bug of CAP3 program. Problem is related to incorrect ACE file generation. Unfortunately we don't have access to CAP3 source code, but I will try to contact the author to report about this problem.

Meanwhile we will prepare a workaround for this issue, based on analysis of "native" output of CAP3. I will update this thread when the fix is ready.

Please note, although the reverse complement reads are not included into the resulting alignment, the contig sequence is correct.

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Reply #2 - Aug 22^nd, 2011 at 6:39pm

Konstantin Okonechnikov Offline
Global Moderator

Posts: 173

On MacOS the behavior is different and related to viewer. And on Windows the CAP3 executable is replaced with newer one.

In result the issue is fully fixed, the bugfix is included into 1.9.6 which is released this week.

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Reply #3 - Aug 23^rd, 2011 at 4:25pm

Rob Offline
YaBB Newbies

Posts: 2

Hi Konstantin,

I will upgrade to 1.9.6.

Thanks for looking into the problem and thanks for providing a great tool for us all.

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Reply #4 - Feb 20^th, 2012 at 10:50pm

Agu Offline
Junior Member
(Argentinian)

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Posts: 63

Oh, sure, no better source to learn than a bug report.

BTW, there should be a way (button?) to easily report spammers or at least a given message as spam...

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Reply #5 - Feb 21^st, 2012 at 3:20am

Konstantin Okonechnikov Offline
Global Moderator

Posts: 173

Quote:

Oh, sure, no better source to learn than a bug report.

BTW, there should be a way (button?) to easily report spammers or at least a given message as spam...

+1

AFAIK forum is being updated frequently, but it looks like it doesn't help

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