This module provides functionality to perform RNASeq analysis to enable users to quantify gene expression, identify splice junctions and measure differential expression using the Tuxedo suite of tools.

Code coverage: (develop branch)

Examples of tools that will be developed in this module:

1. Associate Reads to RNASeq Sample

2. Build Bowtie2Index

3. Align Reads to Tophat

4. Align Reads to Bowtie2

5. Compute Gene Expression -Cufflinks

6. Merge transcripts to Transcriptome - Cuffmerge

7. Identify Differential Expression - Cuffdiff

8. Create ExpressionSeries

9. Create ExpressionMatrix

10. View Expression Histogram

11. View Alignment Statistics - Pie Chart

1. Delete the PATHONPATH in the 'bin/run_KBaseRNASeq.sh'

2. . /kb/dev_container/user-env.sh

3. export PYTHONPATH='kb/deployment/lib'

4. insert 'token=token.rstrip()' in line526 within lib/biokbase/RNASeq/KBaseRNASeq.py

5. make deploy

6. testing the command: ./bin/run_KBaseRNASeq.sh test/script_test/input.json output.txt /mnt/project/mytoken.txt

Trapnell C,et al. 2009 TopHat: discovering splice junctions with RNA-Seq.Bioinformatics

Trapnell C,et al. 2010 Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation.Nature Biotechnology

Kim D, et al. 2011 TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biology