PE mode vs SE mode

[Paul]

Hello,

I am currently trying to analyze more than 150 samples with Trust. It happens a lot that samples have a too small insert size and it switches automatically to SE mode. I want to keep the analysis consistent between the samples and also want the maximum of the detectable CDR3 sequences. Therefore, I have run Trust on some samples one time in SE mode (-s) and one time in PE mode (by setting -I 200) for comparison of the performance of the two methods. The results have a big overlap but there are still some CDR3 sequences found with one mode which were not found with the other. Would you recommend to merge the results from PE and SE? Is it best to let Trust decide which mode to use? Thank you in advance.

By the way: What does the parameter -a stands for? Unfortunately it is not stated in the --help output

Best wishes,
Paul

[Bo Li]

Hi Paul,

Thank you for using our method. I would recommend PE mode as long as you can run it through. 

-a is a legacy option for generating fasta format. It is no longer used in TRUST3.

Thanks,

Bo

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