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Title:	NGS Course Resources
Author:	Anna M Battenhouse	May 16, 2012
Last Changed by:	Anna M Battenhouse	May 21, 2013
Tiny Link: (useful for email)	https://wikis.utexas.edu/x/qg8GAg
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Bioinformatics Team (BioITeam) at the University of Texas (7)     Page: Genome Variant Analysis Course 2015     Page: Genome Variant Analysis Course 2014     Page: Differential expression with splice variant analysis aug2012     Page: Handling Sequences Overview     Page: SSC Intro to NGS Bioinformatics Course     Page: Obsolete NGS course materials     Page: Resources

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External Links (47)
    ftp://gapdh.icmb.utexas.edu/ssi_ngs/BEDTools-User-Manual.v4…
    www.ncbi.nlm.nih.gov/sra
    samtools.sourceforge.net/
    www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/v…
    www.nilshomer.com/index.php?title=NGS_Alignment
    genome.ucsc.edu/cgi-bin/hgTables
    cufflinks.cbcb.umd.edu/
    hannonlab.cshl.edu/fastx_toolkit/
    www.seqan.de/projects/mason/
    www.ncbi.nlm.nih.gov/books/NBK56560/
    bio-bwa.sourceforge.net/
    genome.ucsc.edu
    www.youtube.com/watch?v=bFNjxKHP8Jc
    media.invitrogen.com.edgesuite.net/ab/applications-technolo…
    code.google.com/p/cutadapt/
    https://wikis.utexas.edu/display/GSAF/Illumina+-+all+flavor…
    korflab.ucdavis.edu/unix_and_Perl/
    www.ncbi.nlm.nih.gov/Traces/sra/?view=software
    www.broadinstitute.org/gsa/wiki
    www.bioinformatics.babraham.ac.uk/projects/fastqc/
    hgwdev.cse.ucsc.edu/
    hgwdev.cse.ucsc.edu/FAQ/FAQformat.html
    seqanswers.com/forums/showthread.php?t=4589
    www.nature.com/nprot/journal/v7/n3/full/nprot.2012.016.html
    ftp://gapdh.icmb.utexas.edu/ssi_ngs/bfast-book.pdf
    samtools.sourceforge.net/SAM1.pdf
    lh3lh3.users.sourceforge.net/NGSalign.shtml
    www.tjhsst.edu/%7Edhyatt/superap/unixcmd.html
    http:bowtie-bio.sourceforge.net/
    seqanswers.com/
    tophat.cbcb.umd.edu/
    www.1000genomes.org/
    ged.msu.edu/angus/tutorials-2012/index.html
    bowtie-bio.sourceforge.net/bowtie2
    usegalaxy.org/
    picard.sourceforge.net/explain-flags.html
    samstat.sourceforge.net/
    cufflinks.cbcb.umd.edu/igenomes.html
    sourceforge.net/apps/mediawiki/bfast
    korflab.ucdavis.edu/Unix_and_Perl/unix_and_perl_v2.3.4.pdf
    en.wikipedia.org/wiki/FASTQ_format
    www.broadinstitute.org/software/igv/download
    vcftools.sourceforge.net/specs.html
    loving.corral.tacc.utexas.edu/bioiteam/general/BEDTools-Use…
    picard.sourceforge.net/
    www.youtube.com/watch?v=77r5p8IBwJk
    www.youtube.com/watch?v=NHCJ8PtYCFc

Bioinformatics Team (BioITeam) at the University of Texas (2)     Page: SRA toolkit     Page: Getting started with Unix and Perl