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RNA-seq workflow

    RNA-seq workflow

    Aug 31, 2011

    This workflow runs tophat on a fastq file, followed by cufflinks

    Import the workflow here: http://prandtlseq.icmb.utexas.edu/u/dhivyaa/w/rna-seq-workflow

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    Bioinformatics Team (BioITeam) at the University of Texas
    • File lists
      File lists
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    • How-to articles
      How-to articles
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    Results will update as you type.
    • Cufflinks
    • Data compression programs
    • Extracting barcode split data from SOLiD 5500 XSQ files
    • FastQC
    • Fastx Toolkit
    • Galaxy Setup
    • Geneid
    • General parser scripts
    • Generation of gene counts from results of mapping to genome
    • Generation of wig files from mapreads output
    • GeneWise
    • Genome Analysis Tool Kit
    • Getting an account on GSAF server-fourierseq
    • Get Tm (melting temperature), length, and %GC from a bunch of sequences
    • glimmer3
    • GMAP and GSNAP
    • Graphic programs
    • GS Amplicon variant analyzer
    • GS De novo assembler
    • GS Reference mapper
    • GS Run processor and run browser
    • Hmmer
    • IGV
    • Make a quick venn diagram based on lists in 3 files
    • mapreads
    • MAQ
    • MaqView
    • Median polish to consolidate quantitations
    • MegaMapper
    • MeV
    • MIRA
    • Mosaik
    • muscle
    • Phred, Phrap, Consed, cross_match, daev
    • Picard
    • Plot a read length histogram based on sequences in a fasta file
    • Python Library
    • Quick tips on GO analysis
    • R and R packages
    • Reverse complement for fasta files
    • RNA-seq workflow
    • SAMTOOLS
    • Sff file manipulation tools
    • SHRiMP
    • Small rna analysis
    • Small-rna data analysis
    • Small RNA Pipeline
    • SOAP
    • SOAPtrans
    • Tips for working with TACC resources
    • Tophat- Cufflinks
    • Tophat-Cufflinks-Cuffdiff, allowing for novel transcripts
    • Tophat-Cufflinks-Cuffdiff, ignoring novel transcripts
    • Tricks to preprocess SOLiD and 454 data
    • Trinity
    • Variant calling
    • Velvet
    • ZOHO Information
    • Removing duplicates from alignment output
    • SAMStat
    • TACC Lonestar workflow scripts
    • Get FASTQ Format
    • launcher_creator.py
    • Wrappers For TACC
    • ssh - generating keys
      Calendars
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