454 transcriptome analysis

[CHRYSES]

Hi,

I have a question regarding the 454 transcriptome (cdna) analysis.

Would it be correct to assume that a 454AllContigs.fna in newbler cDNA assembly directory is a non-redundant version of -all- the reference bases that are in the 454Isotigs.fna file?

I would like to carry out a read mapping on a set where there are no exons in multiple isotigs but is represented only once (in contigs) so that the mapping quality is kept high when using bwa bwasw.


Thanks for answers.

[flxlex]

That would have been nice, now, wouldn't it.... Unfortunately, depending on your sample, you might find very similar contigs with just a few base changes between them. Small sequence variations can cause this behavior. Perhaps in the ideal case of all samples coming from the same organism that in addition is homozygous on all loci (e.g. haploid or double haploid) would you find unique contigs only.

To make a non-redundant contig dataset would require clustering (using CD-HIT or other tools), within isogroups perhaps.