Convert NCBI SRA data to gene expression data
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6.0 years ago
Eric Wang ▴ 50

I have downloaded some SRA data from NCBI(GEO)? I converted SRA data into fastq format. I want to know how to convert fastq format to Gene Expression Matrix using STAR, RSEM?

alignment RNA-Seq genome NCBI • 2.4k views
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6.0 years ago
GenoMax 148k

Mapping of reads with STAR : https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4631051/ (consult STAR manual for latest changes).
RNAseq expression analysis using DESeq2: https://www.bioconductor.org/packages/devel/workflows/vignettes/rnaseqGene/inst/doc/rnaseqGene.html
RSEM Tutorial: https://github.com/bli25broad/RSEM_tutorial

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