1. Project progress
Brachypodium
Rodenburg
Wang
Muminov
Karrenbelt

2. Project Planning TopHat, Cufflinks and Cuffmerge [M]
Cuffdiff [S] ==> [C]
Select top & bottom 100 expressed genes [M]
Analyse [M]
Conserved regions and upstream motifs [C]
Cytoscape network inference [C] ==> [S]
GO enrichment analysis [W] ==> [S]
Analyse: transcript length, GC content, intron length, codon usage
Make a table out of this

3. Results so far Tophat.pl and Cufflinks.pl transcripts.gtf into fasta
Analysis.pl containing subs for:
Transcript length, GC content, translation
Test file in fasta format used for verification
Instead of using cuffmerge to create merged.gtf the average FPKM is calculated from the transcript.gtf files in order to select top and bottom 100 genes

4. Flowchart FastQ files TopHat Mapped reads Cufflinks
Assembled transcripts
R Analysis
Average FPKM
Codon bias
Translate
GC content
Analyse
Fasta files
Fasta formatter
Select genes
Transcript length
Intron length
Transcript features
Transcript ID
Cellular component
Molecular function
GO enrichment
Network
Cytoscape
Biological process

5. Future perspective Tasks Assigned to Pipeline assembly Sander
R scripting
Bob
Codon bias
Michiel
Network inference & GO
Simon
Verification
MEME analysis
SignalP
Finish all Must haves
Including intron length and codon bias
Use modules instead of merging scripts
Avoid confounding of variables etc.
MEME, SignalP, alternative initiation codons, overlapping genes

6. Issues and Challenges Top 100 transcripts ≠ top 100 genes
Analysis of isoforms
Cusp package
Cytoscape into the pipeline?
Verification
Cusp: command requires file input, thus we cannot write 1 file containing all 100 sequences, rather have to write 100 files and loop through these
Verification: literature, protein BLAST