[mira_talk] difficulty with convert_project
- From: Jeremy Volkening <volkening@xxxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Sun, 02 Jan 2011 14:06:48 -0600
Hi,
I'm new to this list and relatively new to mira, but it seems like a
really nice tool. Assembling using mira and gap4 is quite smooth.
I've run into unexpected behavior, however, going from gap4 back to
mira. I have a project with only 454 FLX reads, with an average coverage
of ~20x. After editing in gap4, I'm using gap2caf and then
convert_project to get a TCS file which I'm parsing to get coordinates
of areas of low coverage (as defined by me). I thought this was working
fine, but started to notice small discrepancies between the unpadded
base coordinates in the TCS file and the coordinates in my consensus
fasta file exported from gap4. To investigate I used convert_project to
create a FASTA consensus file from the CAF file and compared this to the
one generated by gap4. There were indeed differences (though small)
between the two.
The only conclusion I can draw from this is that convert_project is
recalculating the consensus, even though I haven't asked it to. I did
notice in the docs that this behavior is forced if there is more than
one strain present (which I'm not certain I understand the logic
behind), but I only have one strain defined in my project. If I don't
specifically tell convert_project to recalculate the consensus,
shouldn't it be identical to the one I get from gap4?
I checked the differences in the consensus files, and the gap4 consensus
appears "correct" while mira is miscalculating the consensus in a few
relatively clean, uncomplicated places. I don't have a problem with this
- I'm just using the gap4 consensus - but I'm wondering if there is a
way to prevent convert_project from re-calculating it, or if there's
something else going on here that I'm not realizing.
I'm using mira v3.2.1. Any help would be appreciated. Thanks,
Jeremy
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