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liuzhenyu-yyy / SCAN-seq2

Code for "High-throughput and high-sensitivity full-length single-cell RNA-seq analysis on third-generation sequencing platform" paper. Pipeline for SCAN-seq2 data processing.
https://www.nature.com/articles/s41421-022-00500-4
MIT License
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salmon cDNA #4

Open JingGuo1997 opened 11 months ago

JingGuo1997 commented 11 months ago

Hi Zhenyu，

I noticed in the script S02.umi.process.one.sh, you used minimap2 for mapping to the reference genome and then used salmon for quantification. Additionally, it seems that for the reference genome, you selected 'cdna' instead of 'dna', and I observed this is related to salmon, as note in the documentation(https://salmon.readthedocs.io/en/latest/salmon.html). However, I seem to be unable to find the rationale behind this choice. Do you know the reason for this?

Sincerely look forward to your reply！

liuzhenyu-yyy commented 11 months ago

Hi Jing,

Mapping to reference cDNA helps distinguish different isoforms of the same genes, which is difficult if reads are mapped to genome reference.

JingGuo1997 commented 11 months ago

Hi Jing,

Mapping to reference cDNA helps distinguish different isoforms of the same genes, which is difficult if reads are mapped to genome reference.

Thank you for your response. It has been immensely helpful of my understanding of third-generation sequencing alignment.