10X邮件列表||前体mRNA比对反义链比例增加

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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 。

Refer to https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/advanced/references#header

【web_summary.html 】 attached.

Thanks.

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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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