On Donnerstag 10 Juni 2010 Davide Scaglione wrote:
Is there any way to tell MIRA to join reads/build contigs only if a
certain
number of reads is producing the join?
No-can-do.
Making an example with my dataset, I'm assembling 1500000 454-EST;
expecially for very large contigs, there are chimera reads that wrongly
join two different big piled-up chunks of reads, coming from different
genes. And this is bad..for annotation and for everything else. Let me
say, a big contig with a 25 x coverage, another contig with 25 x
coverage,
joined by only one read on the middle...of course a NCBI blastx reveal
that it's a misassembly.
There may be a way out of the situation, but it's probably associated to
loss
of data: chimera detection.
You have this:
r1 xxxxxxxxxxxxxxxx
r2 xxxxxxxxxxxxxxxxx
r3 xxxxxxxxxxxxxxxxx
r4 xxxxxxxxxxxxxxxxxxooooooooooooo
r5 ooooooooooo
r6 ooooooooooo
r7 ooooooooo
with r4 being the chimera. The chimera detection in MIRA works by
searching
for sequence stretches which are not covered by overlaps. If you now use
the
chimera detection of MIRA, it will almost certainly flag r4 as chimera and
only use a part of it (x or o, depending of which part is longer). There
is
always a chance that r4 is a valid read though, but that's a risk to take.
Now, that would be totally fine, if one would not have to account for
lowly
expressed genes. Imagine this situation:
s1 xxxxxxxxxxxxxxxxx
s2 xxxxxxxxxxxxxxxxxxxxxxxxx
s3 xxxxxxxxxxxxxxx
Look at s2; from an overlap perspective, s2 could also very well be a
chimera,
leading to a break of an otherwise perfectly valid contig. This is why
chimera
detection is switched off by default in MIRA.
Because setting only a fixed integer as parameter might be a problem for
low-coverage contigs/regions; an idea could be to set a drop-on-coverage
on which MIRA split contigs....e.g.: on regions were the coverage drop
under a certain percentage of the average of the contig (or better, of a
the previous windows of let say, 50 bp).
A similar idea has been for quite some time on my TODO, but I never came
around investigating it further, sorry.
At the moment, the only thing you can do is to write a parser for
searching
these kind of things in a contig, extract the corresponding reads and re-
assemble them with chimera detection switched on.
Regards,
Bastien
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