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The other option is to hunt for a working ACE to SAM/BAM converter which handles the paired information - people have tried this before but I'm not sure if there is a complete solution.
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Originally posted by maubp View PostYou could also try 454 assembly with MIRA4 which has SAM output (or you can convert MIRA's own output into SAM).
But I agree, .. with MIRA4 you gain more flexibilty. E.g. Staden's gap4/5 :-)
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You could also try 454 assembly with MIRA4 which has SAM output (or you can convert MIRA's own output into SAM).
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Originally posted by maubp View PostYou'd have to convert your assembly into SAM/BAM if you want Tablet (or most other assembly viewers) to show the pairing. That conversion might be possible with GAP5...
Also Newbler had some experimental BAM output support - I'm not sure if it was ever properly finished and working though.
Thanks for the advice.
S.
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Originally posted by susanklein View PostI have a 454 dataset of 'allcontigs.ace'. The reads consist of paired and unpaired. If I use a viewer like Tablet, which I find very good.. I can see the paired reads in the contigs and which other contigs they are paired to etc.
Also Newbler had some experimental BAM output support - I'm not sure if it was ever properly finished and working though.
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Thanks Sven, I followed the consed docs on installation and wasted a day in the attempt.. error after error.. so don't have time for it. Need results. I'll try the other progs.
Thx again.
S.
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If you want to edit the assembly (e.g. move contigs around etc.) I'd recommend consed. Installation is not really complicated and very well documented. Newbler, gsAssembler, is able to produce a complete consed folder. This has to be checked before the actual (denovo) assembly.
If it is just for viewing the paired reads information / contig layout, Hawkeye is the way to go :-)
my 2p,
Sven
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Hi,
I tried Eagle, Consed (couldn't install), Tablet, Magicviewer. Tablet does show the orietation of each paired read.. The more I think about it, that should be enough, but it would be nice to view the 'joined' contigs together. I will try amos.
Thanks,
S.
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What viewers have you tried?
Have you tried Hawkeye, it is part of the Amos package?
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454 ACE assembly with paired reads... how to view?
Hi,
I'm new here, thanks in advance for any help.
I have a 454 dataset of 'allcontigs.ace'. The reads consist of paired and unpaired. If I use a viewer like Tablet, which I find very good.. I can see the paired reads in the contigs and which other contigs they are paired to etc. but I cannot see the corresponding orientation of those contigs.. I should say, I am trying to examine a 'chain' of contigs out from one of interest, none of which have been included in the scaffold (because they originate from a 16S sequence). So my question is.. is there a viewer I can use which will show the contigs and their relative orientation, based on the paired reads they share?
I have tried several so far with no luck.
Thanks very much,
S.
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