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xiaoyonf
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@xiaoyonf-11632
Last seen 7.5 years ago
Hello,
I have a unannotated lncRNA seq (~2K) that was identified by a study from online literature. I want to use the RNA-seq data (e.g., TCGA) to quantify this lncRNA expression in different samples. How can I do this?
Thank you for answers!@
Xiaoyong
I think you can add the co ordinates and info into the annotation file with your genome and run RSEM and use their TPM to quantify between different samples
Sounds great! I will try RSEM. Thanks for this answer.
Xiaoyong
Thank you, chris86. May I ask you one more question. The RSEM seems to need to be run on server. May I use my Mac Pro notebook to run this software? Thanks again!
Xiaoyong
You would have to check the specifications on the RSEM website. The package EXPRESS is also good for expression quantification and is based on RSEM.
It may take too long to run on your laptop depending on the number of reads you have. People usually use a cluster or high performance desktop.
You can make a feature request at cBioPortal's issue tracker. It would be convenient to be able to provide genomic coordinates and easily create a visualisation of gene expression across many samples within and between cancers.