Question: stringtie + ballgown for multivariate analysis of rna-seq data
2
gravatar for nancy
2.4 years ago by
nancy80
nancy80 wrote:

I have RNA-seq data from 2 different genotypes, and each includes a treated versus mock-control. I'd like to use the hisat2+stringtie+ballgown pipeline to identify D.E. genes between the two genotypes, in treated vs control.

I am unable to come up with the right stattest argument to code for this.

For e.g. if my phenotype file is as follows: (design does include 3x replicates)

SAMPLE(name) GENOTYPE (KO or WT) TREATMENT (COMPOUND or MOCK)

And I use stattest (bg, feature = "transcript", covariate = "GENOTYPE", adjustvars = c("TREATMENT"), getFC = TRUE, meas = "FPKM") I'm afraid I'm going to get all the transcripts that are D.E in KO vs WT, regardless of whether they have been treated with Compound or mock.

Whereas what I want is all transcripts D.E. in KO vs WT, specifically when treated with COMPOUND (not when treated with MOCK).

Thanks in advance for reading,

ADD COMMENTlink modified 2.4 years ago • written 2.4 years ago by nancy80
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 705 users visited in the last hour