Difference between revisions of "1.1 RNA-Seq analysis tools"

From IBERS Bioinformatics and HPC Wiki
Jump to: navigation, search
 
(21 intermediate revisions by the same user not shown)
Line 3: Line 3:
 
{| class="wikitable"
 
{| class="wikitable"
 
|-
 
|-
−
! Tool !! Type !! URLs
+
! scope="col"| Tool
 +
! scope="col"| Category
 +
! scope="col"| URLs
 +
|-
 +
! scope="row"| FASTQC
 +
|Home
 +
| http://www.bioinformatics.babraham.ac.uk/projects/fastqc/
 +
|-
 +
! scope="row"|
 +
|Program
 +
| http://sourceforge.net/projects/bowtie-bio/files/bowtie2/2.2.6/
 +
|-
 +
! scope="row"|
 +
|Manual
 +
| http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml
 +
|-
 +
 
 +
! scope="row"| Trimmomatic
 +
|Home
 +
| http://www.usadellab.org/cms/?page=trimmomatic
 +
|-
 +
! scope="row"|
 +
|Program
 +
|  http://www.usadellab.org/cms/?page=trimmomatic
 +
|-
 +
! scope="row"|
 +
|Manual
 +
| http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/TrimmomaticManual_V0.32.pdf
 +
|-
 +
 
 +
! scope="row"| Bowtie2
 +
|Home
 +
| http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
 +
|-
 +
! scope="row"|
 +
|Program
 +
| http://sourceforge.net/projects/bowtie-bio/files/bowtie2/2.2.6/
 +
|-
 +
! scope="row"|
 +
|Manual
 +
|http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml
 +
|-
  
 +
 +
! scope="row"| TopHat
 +
|Home
 +
| https://ccb.jhu.edu/software/tophat/index.shtml
 +
|-
 +
! scope="row"|
 +
|Program
 +
| https://ccb.jhu.edu/software/tophat/manual.shtml
 +
|-
 +
! scope="row"|
 +
|Manual
 +
|https://ccb.jhu.edu/software/tophat/downloads/tophat-2.1.0.tar.gz
 
|-
 
|-
−
| rowspan="2" | FASTQC
 
  
−
| colspan="2" style="text-align: center;" | Home
+
! scope="row"| Cufflinks
−
| colspan="2" style="text-align: center;" | http://www.bioinformatics.babraham.ac.uk/projects/fastqc/
+
|Home
−
| colspan="2" style="text-align: center;" | Program
+
| http://cole-trapnell-lab.github.io/cufflinks/
−
| colspan="2" style="text-align: center;" | Manual
+
|-
 +
! scope="row"|
 +
|Program
 +
|http://cole-trapnell-lab.github.io/cufflinks/install/
 +
|-
 +
! scope="row"|
 +
|Manual
 +
|http://cole-trapnell-lab.github.io/cufflinks/manual/
 +
|-
 +
 
 +
 
 +
! scope="row"| STAR
 +
|Home
 +
| https://github.com/alexdobin/STAR
 +
|-
 +
! scope="row"|
 +
|Program
 +
|https://github.com/alexdobin/STAR/releases
 +
|-
 +
! scope="row"|
 +
|Manual
 +
|https://github.com/alexdobin/STAR/blob/master/doc/STARmanual.pdf
 +
|-
 +
 
 +
 
 +
! scope="row"| BWA
 +
|Home
 +
| http://bio-bwa.sourceforge.net
 +
|-
 +
! scope="row"|
 +
|Program
 +
|http://sourceforge.net/projects/bio-bwa/files/
 +
|-
 +
! scope="row"|
 +
|Manual
 +
|http://bio-bwa.sourceforge.net/bwa.shtml
 +
|-
 +
 
 +
 
 +
! scope="row"| Velvet
 +
|Home
 +
|https://www.ebi.ac.uk/~zerbino/velvet/
 +
|-
 +
! scope="row"|
 +
|Program
 +
|https://www.ebi.ac.uk/~zerbino/velvet/velvet_1.2.10.tgz
 +
|-
 +
! scope="row"|
 +
|Manual
 +
|https://www.ebi.ac.uk/~zerbino/velvet/Manual.pdf
 +
|-
 +
 
 +
 
 +
! scope="row"| Samtools
 +
|Home
 +
|http://samtools.sourceforge.net
 +
|-
 +
! scope="row"|
 +
|Program
 +
|http://sourceforge.net/projects/samtools/files/
 +
|-
 +
! scope="row"|
 +
|Manual
 +
|http://www.htslib.org/doc/samtools.html
 +
|-
 +
 
 +
! scope="row"| Varscan
 +
|Home
 +
|http://varscan.sourceforge.net
 +
|-
 +
! scope="row"|
 +
|Program
 +
|http://sourceforge.net/projects/varscan/files/
 +
|-
 +
! scope="row"|
 +
|Manual
 +
|http://varscan.sourceforge.net/using-varscan.html
 
|-
 
|-
−
| C <!-- column 1 occupied by cell Tool -->
 
  
 
|}
 
|}
 +
 +
 +
For a more complete overview of next generation sequencing software tools required for
 +
basic pipelines and for more advanced analysis see:
 +
http://seqanswers.com/wiki/Software/list

Latest revision as of 21:00, 24 January 2016

The table below provides the tools for RNA-Seq analysis that you will use in this tutorial.

Tool Category URLs
FASTQC Home http://www.bioinformatics.babraham.ac.uk/projects/fastqc/
Program http://sourceforge.net/projects/bowtie-bio/files/bowtie2/2.2.6/
Manual http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml
Trimmomatic Home http://www.usadellab.org/cms/?page=trimmomatic
Program http://www.usadellab.org/cms/?page=trimmomatic
Manual http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/TrimmomaticManual_V0.32.pdf
Bowtie2 Home http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
Program http://sourceforge.net/projects/bowtie-bio/files/bowtie2/2.2.6/
Manual http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml
TopHat Home https://ccb.jhu.edu/software/tophat/index.shtml
Program https://ccb.jhu.edu/software/tophat/manual.shtml
Manual https://ccb.jhu.edu/software/tophat/downloads/tophat-2.1.0.tar.gz
Cufflinks Home http://cole-trapnell-lab.github.io/cufflinks/
Program http://cole-trapnell-lab.github.io/cufflinks/install/
Manual http://cole-trapnell-lab.github.io/cufflinks/manual/
STAR Home https://github.com/alexdobin/STAR
Program https://github.com/alexdobin/STAR/releases
Manual https://github.com/alexdobin/STAR/blob/master/doc/STARmanual.pdf
BWA Home http://bio-bwa.sourceforge.net
Program http://sourceforge.net/projects/bio-bwa/files/
Manual http://bio-bwa.sourceforge.net/bwa.shtml
Velvet Home https://www.ebi.ac.uk/~zerbino/velvet/
Program https://www.ebi.ac.uk/~zerbino/velvet/velvet_1.2.10.tgz
Manual https://www.ebi.ac.uk/~zerbino/velvet/Manual.pdf
Samtools Home http://samtools.sourceforge.net
Program http://sourceforge.net/projects/samtools/files/
Manual http://www.htslib.org/doc/samtools.html
Varscan Home http://varscan.sourceforge.net
Program http://sourceforge.net/projects/varscan/files/
Manual http://varscan.sourceforge.net/using-varscan.html


For a more complete overview of next generation sequencing software tools required for basic pipelines and for more advanced analysis see: http://seqanswers.com/wiki/Software/list

Retrieved from "https://bioinformatics.ibers.aber.ac.uk/wiki/index.php?title=1.1_RNA-Seq_analysis_tools&oldid=393"