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GoekeLab / sg-nex-data

Nanopore RNA-Seq data from the Singapore Nanopore-Expression Project
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Sequin spike-in reference #45

Closed zzare-umd closed 9 months ago

zzare-umd commented 10 months ago

Hi,

My advisor, @rob-p, and I are currently utilizing the SG-NEx dataset for the evaluation of our quantification model. In the course of our research, we came across a reference in the paper "https://doi.org/10.1101/2021.04.21.440736," where it is mentioned that, "For a subset of sequencing runs, we included sequin spike-in RNAs with known concentrations that enable the evaluation of transcript discovery and quantification."

We have been searching for resources that provide information about which specific dataset within SG-NEx contains the sequin spike-in data, as well as the corresponding concentrations of these spike-ins. However, our efforts thus far have not yielded the desired information.

Any guidance or information in locating the source or reference that specifies the dataset containing the sequin spike-in data and their respective concentration values within the SG-NEx dataset would be greatly appreciated.

Regards, Zahra

rob-p commented 9 months ago

Hi @jonathangoeke,

I just wanted to ping back about this. It would be super useful to us (and I think several others using this data), if the sample sheets contained the info about what samples included the spikeins and in which ratios.

Thanks, Rob

cying111 commented 9 months ago

Hi @zzare-umd and @rob-p

really sorry for getting back so lately! We have updated the sample spreadsheet with one additional column that indicates the spike-in concentration usage and also included a section in data release and access here with the true concentration file locations. Please check those out and let us know if you have any problems in accessing these files or additional questions regarding spike-in reference!

Thank you! Ying

rob-p commented 9 months ago

Dear Ying,

Thank you so much! This will be very helpful. And thank you again for curating this amazing dataset and making it available to the community!

Best, Rob & Zahra

cying111 commented 9 months ago

You are most welcome!! I will close this issue then and thank you again for using our data resource and providing your feedback!