Cuffdiff: All three conditions at once v.s. Pair-wise compare?
0
0
Entering edit mode
6.9 years ago
Puriney ▴ 330

I have RNA-seq data under three different environmental experiments with the goal to detect differently splicing transcripts. When dealing with my three conditions, let's cond_x, cond_y, cond_z, I could:

  • Strategy 1: run cuffdiff with all of their alignments as inputs
  • Strategy 2: pair-wise compare. 

I have tried both the strategies, but it turns out that only Strategy 1 would yield differently spliced events in isoform_exp.diff output file while strategy 2 yield nothing different. 

Could anyone give me some information why this happen?

My command line is :

cuffdiff -o out_dir -L Cx,Cy,Cz --library-type fr-firststrand --num-threads 3 \

--frag-bias-correct genome.fa ensembl.annotation.gtf \

Cx_1.bam,Cx_2.bam,Cx_3.bam Cy_1.bam,Cy_2.bam,Cy_3.bam Cz_1.bam Cz_2.bam Cz_3.bam

Cuffdiff • 2.1k views
ADD COMMENT

Login before adding your answer.

Traffic: 2435 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6