Faq

#Frequently Asked Questions

What is the meaning of the name afterParty?

The name reflects the ancestry of the the project. Our last-generation transcriptome analysis tool, built for assembling and annotating Sanger EST datasets, was called PartiGene for Partial Genome. This project comes after Partigene, so it is called afterParty.

Is it better to do the assembly myself and upload it, or upload my raw reads and let afterParty do the assembly?

If you're in a position to assemble your raw reads into contigs yourself, then you will almost definitely get better results by doing it that way. afterParty uses MIRA to assemble raw reads, and uses the default parameters. By doing the assembly yourself, you will have access to a range of different assemblers and can optimize the assembly process for your own data.

Of course, if you have anything other than Roche 454 data (Sanger, Illumina, IonTorrent, PacBio, etc.) then you will need to do the assembly yourself anyway.

Is it better to do the annotation myself and upload it, or let afterParty do the annotation?

If you have the ability to do the BLAST / InterProScan annotation yourself, then it's probably better to do so, and upload the results to afterParty for indexing. Doing the annotation yourself will probably be quicker, especially if you have access to cluster or cloud compute resources. You can also decide exactly which database you want to carry out BLAST searches against, and even use a custom database if you like.