Question: RNA-seq data analysis for differential expression of a single gene
gravatar for nancy
22 months ago by
nancy80 wrote:

I have some RNA-seq data for a large number of samples (treated vs control), to the order of ~50M PE reads per sample, from mouse. These data have not been aligned yet to the reference genome.

I am, however interested in the expression level of one single target gene across all these samples, and a quantification of whether it is differentially expressed between treated and control.

Is there a quick way of doing this, where I can bypass alignment to the whole genome, but only align to the target gene of interest? (An alignment-free method like kallisto/sleuth may be another option, it just occurred to me, but I was wondering more about a brute-force alignment to target method)


rna-seq • 533 views
ADD COMMENTlink modified 22 months ago by JC11k • written 22 months ago by nancy80
gravatar for JC
22 months ago by
JC11k wrote:

Your major problem will be uncertainness of reads mapped to more than one location in the genome/transcriptome, definitively you need to align to the genome or transcriptome to remove non-unique reads or apply some strategy to decide origin. Kallisto, Sleuth or Salmon are fast enough to create your expression tables and then filter your gene.

ADD COMMENTlink written 22 months ago by JC11k
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