annotate README @ 5:60a6f2d92058

Adding Galaxy-Workflow-MMuFF.ga (version 1.4 updated for SnpEff v3.2 and snpeff_cds_report v1.2)
author Jim Johnson <jj@umn.edu>
date Sun, 26 May 2013 08:17:53 -0500
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1 MMuFF: Missense Mutation and Frameshift Finder
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2 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.
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4 The parameter settings in the workflows are set for human samples.
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6 To execute MMuFF create a Galaxy history and upload the four input files:
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7 1. tumor sample forward reads fastq
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8 2. tumor sample reverse reads fastq
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9 3. dbSNP VCF file
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10 4. additional exclusions VCF
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12 Select Galaxy-Workflow-MMuFF_v1.2.ga to Run
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13 Set input files for Galaxy-Workflow-MMuFF_v1.2.ga
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15 If you have reads from matched tumor/normal tissue samples,
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16 run the Galaxy-Workflow-MMuFF_Human_germline_v1.2.ga on the noraml samples with inputs:
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17 1. normal sample forward reads fastq
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18 2. normal sample reverse reads fastq
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19 3. dbSNP VCF file
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20 and use the final VCF as input 4 "additional exclusions VCF" in the Galaxy-Workflow-MMuFF_v1.2.ga workflow.
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