Convert NCBI SRA data to gene expression data · Biostar

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Convert NCBI SRA data to gene expression data

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

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written 7.7 years ago by Eric Wang •

1 answer

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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written 7.7 years ago by GenoMax

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