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mkatari-bioinformatics-august-2013 [2014/06/04 08:10] – mkatarimkatari-bioinformatics-august-2013 [2014/06/04 08:12] – mkatari
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 Manny's workshop: Manny's workshop:
-  * Introduction to Linux -- [[https://docs.google.com/file/d/0B172nc4dAaaOOUdvVlowZHo4R0E/edit?usp=sharing|ppt]] -- [[mkatari-bioinformatics-august-2013-introLinuxNotes|Linux notes]]  +  * Introduction to Linux 
-  * Introduction to Sequence Technology -- [[https://docs.google.com/file/d/0B172nc4dAaaOVGZIQXRWUlRmU1E/edit?usp=sharing|ppt]] -- [[http://hannonlab.cshl.edu/fastx_toolkit/commandline.html|Fastx toolkit]] -- [[http://www.bioinformatics.babraham.ac.uk/projects/fastqc/|Fastqc]]+          * [[https://docs.google.com/file/d/0B172nc4dAaaOOUdvVlowZHo4R0E/edit?usp=sharing|ppt]] 
 +          * [[mkatari-bioinformatics-august-2013-introLinuxNotes|Linux notes]]  
 +  * Introduction to Sequence Technology 
 +          * [[https://docs.google.com/file/d/0B172nc4dAaaOVGZIQXRWUlRmU1E/edit?usp=sharing|ppt]] 
 +          * [[http://hannonlab.cshl.edu/fastx_toolkit/commandline.html|Fastx toolkit]] 
 +          * [[http://www.bioinformatics.babraham.ac.uk/projects/fastqc/|Fastqc]]
   * Introduction to Sequence Alignment   * Introduction to Sequence Alignment
           * [[https://docs.google.com/file/d/0B172nc4dAaaOcHlWZHM5WUw5SFE/edit?usp=sharing|ppt]]           * [[https://docs.google.com/file/d/0B172nc4dAaaOcHlWZHM5WUw5SFE/edit?usp=sharing|ppt]]
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           * [[http://samtools.sourceforge.net/samtools.shtml|Samtools]]           * [[http://samtools.sourceforge.net/samtools.shtml|Samtools]]
           * [[http://mummer.sourceforge.net/manual/|MUMmer]]           * [[http://mummer.sourceforge.net/manual/|MUMmer]]
-  * Visualizing your alignments -- [[mkatari-bioinformatics-august-2013-IGVnotes|IGVnotes]] +  * Visualizing your alignments 
-  * Introduction to Mapping and Sequence Assembly -- [[https://docs.google.com/file/d/0B172nc4dAaaOREpEdVZtSkw5dGs/edit?usp=sharing|ppt]] -- [[http://www.ebi.ac.uk/~zerbino/velvet/Manual.pdf|Velvet Documentation]] -- [[http://seqanswers.com/wiki/ABySS|ABySS]] +          * [[mkatari-bioinformatics-august-2013-IGVnotes|IGVnotes]] 
-  * Introduction to RNA-seq -- [[https://docs.google.com/file/d/0B172nc4dAaaONnVoWWJJdWlkQUU/edit?usp=sharing|ppt]] -- [[http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml|Bowtie2]] -- [[http://tophat.cbcb.umd.edu/manual.shtml|Tophat]] -- [[http://cufflinks.cbcb.umd.edu/manual.html|Cufflinks]] -- [[http://cufflinks.cbcb.umd.edu/manual.html#cuffdiff|CuffDiff]] -- [[ http://www.bioconductor.org/packages/release/bioc/vignettes/DESeq/inst/doc/DESeq.pdf|DESeq manual]] +  * Introduction to Mapping and Sequence Assembly 
 +          * [[https://docs.google.com/file/d/0B172nc4dAaaOREpEdVZtSkw5dGs/edit?usp=sharing|ppt]] 
 +          * [[http://www.ebi.ac.uk/~zerbino/velvet/Manual.pdf|Velvet Documentation]] 
 +          * [[http://seqanswers.com/wiki/ABySS|ABySS]] 
 +  * Introduction to RNA-seq 
 +          * [[https://docs.google.com/file/d/0B172nc4dAaaONnVoWWJJdWlkQUU/edit?usp=sharing|ppt]] 
 +          * [[http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml|Bowtie2]] 
 +          * [[http://tophat.cbcb.umd.edu/manual.shtml|Tophat]] 
 +          * [[http://cufflinks.cbcb.umd.edu/manual.html|Cufflinks]] 
 +          * [[http://cufflinks.cbcb.umd.edu/manual.html#cuffdiff|CuffDiff]] 
 +          * [[ http://www.bioconductor.org/packages/release/bioc/vignettes/DESeq/inst/doc/DESeq.pdf|DESeq manual]] 
  
 Manny's R Lectures: Manny's R Lectures:
mkatari-bioinformatics-august-2013.txt · Last modified: 2017/01/25 05:13 by mkatari