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
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
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