Mercurial > repos > jjohnson > mmuff
diff README @ 2:04e170c09922
Add a workflow for noraml tissue samples.
author | Jim Johnson <jj@umn.edu> |
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date | Fri, 12 Apr 2013 07:51:45 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README Fri Apr 12 07:51:45 2013 -0500 @@ -0,0 +1,21 @@ +MMuFF: Missense Mutation and Frameshift Finder +analyzes Next Generation Sequencing (NGS) paired read RNA-seq output to reliably identify small frameshift mutations, as well as missense mutations, in highly expressed protein-coding genes. MMuFF ignores known SNPs, low quality reads, and poly-A/T sequences. For each frameshift and missense mutation identified MMuFF provides the location and sequence of the amino acid substitutions in the novel protein candidates for direct input into epitope evaluation tools. + +The parameter settings in the workflows are set for human samples. + +To execute MMuFF create a Galaxy history and upload the four input files: + 1. tumor sample forward reads fastq + 2. tumor sample reverse reads fastq + 3. dbSNP VCF file + 4. additional exclusions VCF + +Select Galaxy-Workflow-MMuFF_v1.2.ga to Run +Set input files for Galaxy-Workflow-MMuFF_v1.2.ga + +If you have reads from matched tumor/normal tissue samples, +run the Galaxy-Workflow-MMuFF_Human_germline_v1.2.ga on the noraml samples with inputs: + 1. normal sample forward reads fastq + 2. normal sample reverse reads fastq + 3. dbSNP VCF file +and use the final VCF as input 4 "additional exclusions VCF" in the Galaxy-Workflow-MMuFF_v1.2.ga workflow. +