search

gpertea / stringtie

Transcript assembly and quantification for RNA-Seq
MIT License
378 stars 78 forks source link

More details on -L option #277

Open LehmannN opened 4 years ago

LehmannN commented 4 years ago

Hi, Quick question: what does it imply to use the -L option ? Long reads have multiple differences between datasets so I would like to know how to adapt this option. More precisely, could we reproduce the -L option by a combination of all the other options (eg -j, -m, -g...) ? Thanks

gpertea commented 4 years ago

To answer your latter question: no, -L cannot be simply reproduced by a combination of other parameters. When -L option is provided there is actually a different branch of code running there (specialized bundle processing functions), with its own specific assumptions about the alignment characteristics, the higher error rate etc. (@mpertea may add to this basic answer if needed, as she is the main author who implemented the core algorithms in StringTie including the novel -L code).

LehmannN commented 4 years ago

Thanks @gpertea for your reply. As I'm comparing the output of novel annotations made from long reads and shorts reads, that would be lovely to get more details from @mpertea if possible. Also, do you know if PacBio and Nanopore data are handled the same way with the -L option ?