Very long contigs...real?

[JackieBadger]

Hi,

I wonder if someone can offer some insight.
I have performed an accurate de novo assembly with poly-a/t trimming im Mira 3.9.5
I get all reads assembled, and no singlets, into around 66k contigs. Around 27k of these are large contigs, with the largest being ~25k bases long. This does not make much sense to me as I constructed a 3' target cDNA library (454 FLX). I can envisage multiple open reading frames may create longer transcripts but 25k seems dodgy to me.
Any thoughts?

Best,

Jack

[cliffbeall]

Some mRNAs are >100,000 nt, for example titin. So it's possible.

[krobison]

Also, you could have overlapping transcripts.

I think the next step is to figure out how you might (in)validate these assemblies. BLASTX might give you an idea how many ORFs each contig encodes and whether they show a pattern of alternating strands.