Skip to content

thebenallen/KBaseRNASeq

 
 

Folders and files

NameName
Last commit message
Last commit date

Latest commit

 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 

Repository files navigation

KBaseRNASeq

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.

Build Status

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

Notes for development:

  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

References:

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

About

No description, website, or topics provided.

Resources

License

Stars

Watchers

Forks

Releases

No releases published

Packages

No packages published

Languages

  • Python 98.1%
  • Makefile 1.5%
  • Other 0.4%