Bioinformatics Reading Group

Department of Biological Sciences, Clemson University

Showing posts with label gene prediction. Show all posts
Showing posts with label gene prediction. Show all posts

Sunday, October 28, 2012

Oct. 29, 2012


Topic: Gene Prediction

Discussion leader:  Daniel
Papers: Picardi and Pesole 2010
            Brent 2008
            Andersson et al. 2012 + Supplemental Data

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Labels: gene prediction
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Resources

  • Spring 2013 Schedule
  • Fall 2012 Schedule
  • How Illumina works (slide set)
  • RNAseq experimental design
  • Seqanswers forum

Software: Quality checking and filtering

  • ConDeTri
  • FastQC
  • HomerTools
  • NGS QC Toolkit
  • Prinseq
  • Tagcleaner
  • Trimmomatic

Software: Short read assembly

  • Cufflinks
  • Trinity
  • Allpaths-LG
  • IDBA
  • ABySS
  • trans-ABySS
  • SOAPdenovo
  • Velvet

Software: Genotype-by-sequencing

  • Stacks
  • Tassel

Bioinformatics Educational Sites

  • PLoS educational collection
  • Rosalind
  • EMBL tutorials
  • Boston College genomics course

Wells Lab protocols and scripts

  • In silico whole genome digests
  • Using FastQC to assess read quality
  • Merging left- and right-hand fastq reads
  • Sample bash script for Trinity on Palmetto Cluster
  • Preparing Trinity output for Blast2GO annotation
  • Setting up a local blast database of Trinity contigs
  • Tophat/Cufflinks pipeline

Short Courses and Training

  • Cold Spring Harbor Labs
  • Bioinformatics.org online courses
  • University of Manchester
  • UC Davis Short Course
  • UC San Diego online course
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