Differential Expression

in progress

Contents

• Overview
• Processing Profile
  • Current Default
  • Updates
• Output Files and Formats
  • Cuffcompare
  • Cuffmerge
  • Cuffdiff
• Tutorial
  • List Input RNA-seq Model Ids
  • Define Differential Expression Model

Overview

The differential expression pipeline is modeled after this Nature Protocols publication: Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

Processing Profile

Current Default

id | name | transcript_convergence_name | transcript_convergence_version | transcript_convergence_biotypes | differential_expression_name | differential_expression_version | differential_expression_mask_reference_transcripts | differential_expression_params | summarize_differential_expression_name | summarize_differential_expression_version ---- | ---- | ---- | ---- | ---- | ---- | ---- | ---- | ---- | ---- | ---- | ---- 2760181 | cuffcompare/cuffdiff 2.0.2 protein_coding only | cuffcompare | 2.0.2 | {include_contained => 1,generic_gtf_input => 1,generate_tracking_files => 0,} | protein_coding | cuffdiff | 2.0.2 | rRNA_MT | --quiet --num-threads 4 | cummerbund | 1.99.2

Updates

Output Files and Formats

Cuffcompare

All cuffcompare output files are well documented in the Cufflinks user manual:

http://cufflinks.cbcb.umd.edu/manual.html#cuffcomp_output

Cuffmerge

All cuffmerge output files are well documented in the Cufflinks user manual:

http://cufflinks.cbcb.umd.edu/manual.html#merger_output

Cuffdiff

All cuffdiff output files are well documented in the Cufflinks user manual:

http://cufflinks.cbcb.umd.edu/manual.html#cuffdiff_output

Tutorial

List Input RNA-seq Model Ids

$ genome model list --filter model_groups.id=628a5c99fc6142a2ac9e4999436f1927
ID                                 NAME                                  SUBJECT                               PROCESSING_PROFILE
--                                 ----                                  -------                               ------------------
01cf673288964882b5e778cd198825df   MMAF-TB336_9-TB336_9.prod-rna_seq     MMAF-TB336_9-TB336_9 (2893829978)     December 2013 OvationV2 RNA-seq Candidate 1 (fa715a8529a8485cb25c83a4ec129bcd)
3cb5c05470cd4d189275d1b78c5e58e3   MMAF-TB364_1-TB364_1.prod-rna_seq     MMAF-TB364_1-TB364_1 (2893829971)     December 2013 OvationV2 RNA-seq Candidate 1 (fa715a8529a8485cb25c83a4ec129bcd)
753018364c79459f9e31186f53027d12   MMAF-TB336_4-TB336_4.prod-rna_seq     MMAF-TB336_4-TB336_4 (2893829976)     December 2013 OvationV2 RNA-seq Candidate 1 (fa715a8529a8485cb25c83a4ec129bcd)
9cfc80ed223a4607b8e25ed7041d8dc3   MMAF-TB336_14-TB336_14.prod-rna_seq   MMAF-TB336_14-TB336_14 (2893829979)   December 2013 OvationV2 RNA-seq Candidate 1 (fa715a8529a8485cb25c83a4ec129bcd)
c0383a67d20e4e8c835d804cee00b4cd   MMAF-TB364_6-TB364_6.prod-rna_seq     MMAF-TB364_6-TB364_6 (2893829972)     December 2013 OvationV2 RNA-seq Candidate 1 (fa715a8529a8485cb25c83a4ec129bcd)
c7d72d8dfb5b4c3fb993c3cc2b5b941b   MMAF-TB336_19-TB336_19.prod-rna_seq   MMAF-TB336_19-TB336_19 (2893829980)   December 2013 OvationV2 RNA-seq Candidate 1 (fa715a8529a8485cb25c83a4ec129bcd)
e5de7c412f9f4364a8d6b79ec629c939   MMAF-TB364_20-TB364_20.prod-rna_seq   MMAF-TB364_20-TB364_20 (2893829974)   December 2013 OvationV2 RNA-seq Candidate 1 (fa715a8529a8485cb25c83a4ec129bcd)
e8d8e6779f674bffb102d549c01f8aed   MMAF-TB336_2-TB336_2.prod-rna_seq     MMAF-TB336_2-TB336_2 (2893829975)     December 2013 OvationV2 RNA-seq Candidate 1 (fa715a8529a8485cb25c83a4ec129bcd)
f00207a1783a4be4aedbe5abb66892ad   MMAF-TB336_5-TB336_5.prod-rna_seq     MMAF-TB336_5-TB336_5 (2893829977)     December 2013 OvationV2 RNA-seq Candidate 1 (fa715a8529a8485cb25c83a4ec129bcd)

Define Differential Expression Model

In the example data set we want to compare two condtions, A and B. In group A we have samples 1, 6 an 19. In group B we have 20, 2, 14 and 4. All Models require a subject and in the case of Differential Expression, the subject is typically the species name. The example usage looks like:

 $ genome model define differential-expression --processing-profile='2250671a46ea4ce39f17478d458970f3' --condition-labels-string='A,B' --subject='Mus musculus J:DO' --condition-model-ids-string='3cb5c05470cd4d189275d1b78c5e58e3,c0383a67d20e4e8c835d804cee00b4cd,c7d72d8dfb5b4c3fb993c3cc2b5b941b e5de7c412f9f4364a8d6b79ec629c939,e8d8e6779f674bffb102d549c01f8aed,9cfc80ed223a4607b8e25ed7041d8dc3,753018364c79459f9e31186f53027d12'
'subject', and 'processing_profile' may require verification...
Resolving parameter 'subject' from command argument 'Mus musculus J:DO'... found 1
Resolving parameter 'processing_profile' from command argument '2250671a46ea4ce39f17478d458970f3'... found 1
Created model:
id: 437567dd99d84afd8123839625bfa336
name: Mus musculus J:DO.differential_expression-1
subject: Mus musculus J:DO (2893829959)
processing_profile: December 2013 Differential Expression Candidate 1 (2250671a46ea4ce39f17478d458970f3)