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bcgsc / RNA-Bloom

:hibiscus: reference-free transcriptome assembly for short and long reads
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question about the output #65

Closed huawen-poppy closed 4 months ago

huawen-poppy commented 7 months ago

Hello!! I noticed that the output file rnabloom.transcripts.fa contains only AGCT. I am wondering is the output file cDNA sequence? Or it is the mRNA sequence but replace the U with T?

Thank you very much!

kmnip commented 7 months ago

When the -strand option is used for strand-specific data (e.g. ONT direct RNA), the assembly would contain mRNA sequences. Otherwise, the assembly can be a mix of both orientations.

By default, all U's are replaced with T's. You can use the -uracil option to write U's instead of T's in rnabloom.transcripts.fa. FYI: https://github.com/bcgsc/RNA-Bloom?tab=readme-ov-file#b-assemble-nanopore-direct-rna-sequencing-data

huawen-poppy commented 4 months ago

Thank you very much!