I noticed that the rna_read_offset of CHEMISTRY_SC5P_PE is 26 bp in chemistry.py. But I think the the read1 in SC5P_PE mode should consider the spacer (TSO sequence). I found the retain of spacer squence (TTTCTTATATGGG) will cause some problems in mapping process.
MengweiLi-project
commented
3 years ago
Dear Cellranger team,
I noticed that the rna_read_offset of CHEMISTRY_SC5P_PE is 26 bp in chemistry.py. But I think the the read1 in SC5P_PE mode should consider the spacer (TSO sequence). I found the retain of spacer squence (TTTCTTATATGGG) will cause some problems in mapping process.
https://github.com/10XGenomics/cellranger/blob/a46b275724de6fc18b91792557289b02dc2e4888/lib/python/cellranger/chemistry.py
I don't know if it better to set rna_read_offset of CHEMISTRY_SC5P_PE to 26 + 13 Looking forward to your response.
Best regards, Mengwei