Opinions about using Newbler with the -rip

[dschika]

Hello everybody,

Who has made experiences using Newbler with the -rip option for cDNA assemblies (i.e. also using the -cdna option)? Do you think it's an option that makes your assemblies more 'reliable'?

I observered the following:
- less aligned reads, but not considerably less
- less aligned bases, roughly between 1% and 3%
- drop in the average number of contigs per isotig
- the number of contigs not in isotigs drops a bit. BUT: the overall number of contigs in 454AllContigs.fna drops considerably
- nearly all of the contigs not used in isotigs are 'threshold'-contigs. Only 1 'threshold'-contig was used in an isotig
- more large contigs are produced
(see also: http://seqanswers.com/forums/showthread.php?t=7210 for another experience)

So, I think the option is usefull. Any opinions/experiences?

Cheers,
Thomas

[flxlex]

Many assembler place reads only in one contig, while newbler splits the reads that appear in mutliple contigs, because they form 'edges' between contigs in the graph. The rip option was added to newbler because for people that ran into problems with the multiple placement.

Your observations on the effect of the option are interesting, but what really counts is to what extend the isotigs with or without the -rip option reflect real transcripts and alternative splice variants...

[Jeremy]

Has anyone made any further progress on this?
/ bump