Config file parameters

[hacaoe]

Hi,
I am currently using FLAMES and a few other assemblers (flair and bookend), to compare them against each other and find out, which would be the most optimal one for my data and workflow (drosophila nanopore-sequences). Currently I am facing the issue, that my FLAMES-based transcriptomes are surprisingly small (after correction and filtering roughly 2500 isoforms against flairs 16000), even with the same references and sequencing files. I think, this may be due to the config file, that I honestly just copied from the github. What would you recommend as parameters/what should be changed to perhaps solve this? Would it be appropriate to be less strict and how would I enforce this in the config file?

Best,
Hasan.

[LuyiTian]

FLAMES perform more aggressive filtering than flair and other tools so it is not surprised you get less isoforms. you can change the parameter here:
"Min_sup_cnt":5,
"Min_cnt_pct":0.001,
"Min_sup_pct":0.2,

like reduce the Min_sup_cnt to 3. although the fact that flair just give you 16000 isoform might because of your data is not deeply sequenced. I am not sure what is the normal number you would expect for drosophila though