Comments (3)
Hi Gangcai,
I worked on BRIE, I do not know where you found your two feature files, but I can tell you that -f is a needed argument for BRIE. You can generate your feature file thanks to brie-factor from briekit. But if you want to try quickly, I think from their names that you could use one or the other of your feature files (I would use the filtered one).
Best,
Milan
from brie.
Hi Milan,
Thanks for your reply. Those two files were generated by briekit-factor according to this script provided by Brie https://github.com/huangyh09/briekit/blob/master/example/anno_mouse.sh. The names indicated in the script are mouse_factors.SE.filtered.csv.gz and mouse_factors.SE.lenient.csv.gz respectively. Do you have any suggestion about in which scenario should I use filtered and when to use lenient?
Best,
Gangcai
from brie.
Hi Gangcai,
These two files are according to the Splicing event annotation: SE.filtered.gff3.gz and SE.lenient.gff3.gz. The former is stricter while the latter is more lenient on the length of alternative exon and the distance between TSS or TTS. Normally, I would recommand using SE.filtered.gff3.gz, but if it doesn't include the events you are interested in, then you could use the lenient one or add it manually.
Best,
Yuanhua
from brie.
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