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ucagenomix / sicelore

Single Cell Long Read is a suite of tools dedicated to Cell barcode / UMI assignment and analysis of highly multiplexed single cell Nanopore long read sequencing data.
MIT License
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whether consensus sequences contain reads with poly-T #26

Closed ssscj closed 2 years ago

ssscj commented 3 years ago

Hi, Thanks for developing this useful software. After the 6th step, generating the consensus sequences, will the complementary reads with poly-T be removed ? Do they contribute to the step of computing consensus sequences? Do the consensus sequences contain reads with poly-T?

Thank you,

Chujie

ucagenomix commented 3 years ago

Hi, no polyT do not contribute to consensus sequence calculation, we remove it from the cDNA sequences before consensus compute using poa (v1) or spoa (v2). But there is still some reads that kept the polyA and you can see some consensus sequence having a polyA. It would be better not to have it before consensus sequence remapping because you may increase a preferential mapping to pseudogenes. Cheers, Kevin.

ssscj commented 3 years ago

Thanks for your reply. I have another question that the consensus sequence is the cDNA sequence, so is it reverse complementary with the mRNA sequence and identical to the template strand on the genome? Thank you.

Best wishes, Chujie