Output interpretation

[gchevignon]

Hello,
I found very difficult to understand the whole output of the Bellerophon pipeline.
Is it correct that the ultimate file to look for is transcripts_BEL.fasta?
More precisely I don't understand what are the threshold that the pipeline use to decide what are a good or a bad transcripts_postCDHIT.fasta?
Is it probably based on data present in assembly_score_optimisation.csv in the TRun_PostBellerophon folder?
It would be great to have some insight (in readme for exemple) about what are the data in this type of files (explanation of the different column ...).

Also Bellerophon in unable to run on a cluster node without internet connexion ... are you aware about this behaviour ?
Since big node inside HPC cluster does not have internet connection, this avoid using Bellerophon on big transcriptome > 100M reads ...

Thanks in advance for your reply !

[JesseKerkvliet]

Hi, thanks for reaching out.
Most of the output files are generated by TransRate (http://hibberdlab.com/transrate/), such as the good.transcripts.fasta and bad.transcripts.fasta. The thresholds are determined by TransRate and are not influenced by Bellerophon. You are correct that the final file is the transcripts_BEL.fasta file. I agree it's useful to have more information about the output file, so I will add that to the readme.

I am unaware of the HPC issue you pointed out, so thanks for that. I will be looking into why that is.

[asan-emirsaleh]

Hello!
I agree with @gchevignon in that some explanation would be useful. If you could extend the Readme with these data some things that are to be understood or search for an answer would be a little more clear for users.