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Hank Tu (10x Genomics)
Sep 28, 01:29 PDT
Hi Yunlai,
We observe an increase in the detection of antisense reads with mapping of single nuclei RNA-seq data to the pre-mRNA reference. We are still investigating the sources of this increase. Some of the possible reasons considered for the increase in antisense mapping: genomic DNA contamination, unannotated transcripts, and/ or sample specific (sample integrity or biology). However, up to this point, the investigation has not been conclusive.
Internally, the highest level of antisense mapping we've seen on any of our v3 samples is ~25% and it was on a very poorly prepared sample. Normally, we see ~15%.
Thanks,
Hank
Hank Tu
Staff Software Engineer, Field Operations
[email protected]
7180 Koll Center Parkway, Suite 110
Pleasanton, CA 94566 | 10xgenomics.com
zhou yunlai
Sep 27, 19:04 PDT
dear:
As you guessed, I make transcriptome reference in 【Generating a Cell Ranger compatible "pre-mRNA" Reference Package】 type 。
【web_summary.html 】 attached.
Thanks.
Hi Yunlai,
Thank you for contacting 10x Support.
When you ran cellranger count, what type of transcriptome reference did you use? Was it a pre-mRNA reference by any chance?
To help me troubleshoot the issue, could you please attach the web_summary.html to this ticket?
Thanks,
Hank
Hank Tu
Staff Software Engineer, Field Operations
[email protected]
7180 Koll Center Parkway, Suite 110
Pleasanton, CA 94566 | 10xgenomics.com
zhou yunlai
Sep 27, 08:49 PDT
dear:
when i use 【cellranger count 】to map genome , in the outfile 【web_summary】 file 【Reads Mapped Antisense to Gene】 about 15% 。 In empirically ,【Reads Mapped Antisense to Gene】 should be less than 5% . i want to know why , in other way , what should I check?
best.
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