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Custom Reference genome SARS-COV-2 #2

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preetida opened this issue Jul 8, 2020 · 0 comments
Open

Custom Reference genome SARS-COV-2 #2

preetida opened this issue Jul 8, 2020 · 0 comments

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@preetida
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preetida commented Jul 8, 2020

Hello,

I recently read your work on BioRixv about SARS-CoV-2 infection in lung epithelial cells. https://www.biorxiv.org/content/10.1101/2020.05.06.081695v1
Nice piece of work! Congratulations.

I was wondering if you can share information about the custom reference you have used in the study.

"The human genome, Ensembl GRCh38.98.gtf, and the SARS-CoV-2 genome, NCBI Genome database accession MT020880.1, were combined and used for alignment."

I am working on a similar project where I am analyzing scRNA(10x) data from cells infected with SARS-CoV2. For finding viral reads in the samples, I have built the custom reference genome by creating a single GTF sequence from MT020880.1 and labeled it as an exon. Custome reference was built by inserting this SARS-CoV-2 gtf to the HG38 gtf. Later I aligned the reads [scRNA data: cells infected with SARS-CoV2] with cellranger. However, I do not see the viral expression in the count matrix.
Did you add each ORF (10 different ORFs) as an individual gtf from the SARS-CoV sequence?

I was wondering if you can share the custom reference genome (GRCh38.98 + MT020880.1 gtf) , it would be very helpful for me to troubleshoot my analysis.

Please feel free to drop me a message at [email protected]

Thank you,
Sincerely,
Preeti

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