Use TRUST4 on selected RNAseq data

[cui jie]

Hello,

I understand that TRUST4 is specifically designed to handle unselected RNAseq data. I have attempted to use TRUST4 to assemble the complete BCR sequence from target enriched BCRseq PE300 data, and it takes approximately 10 hours to process 16 million reads. I would like to know if you have any recommendations for optimizing the parameters of TRUST4 to improve its speed, or if I should consider using an alternative method for this purpose. Thank you for your assistance.

[Li Song]

For targeted amplified data, you may add the option "--repseq" to accelerate the program. Is your data also UMI-based?

[cui jie]

@mourisl Thanks for the advice, will try it. For now, my data is not UMI-based. If so, I'll specify the UMI file when running it, right? Is there anything I need to pay attention to?

[Li Song]

If your data is UMI-based bulk BCR-seq, you can use the option "--barcode UMI_file.fa --barcodeLevel molecule --readFormat XXX".

[cui jie]

Thanks a lot, I'll close this issue.