The ncPRO-seq pipeline requires the following additional softwares. Please refer to section 7 for more details :
- The http://bowtie-bio.sourceforge.net/manual.shtml Bowtie Aligner (
v2.0) [9] to align the reads from smallRNA-seq data.
- The http://www.r-project.org/ R (
v2.12.0) [13] and http://www.bioconductor.org/ BioConductor [6] softwares.
- The R packages: http://www.bioconductor.org/packages/2.2/bioc/html/seqLogo.html seqLogo [2], http://www.bioconductor.org/packages/2.6/bioc/html/girafe.html girafe [16] and http://cran.r-project.org/web/packages/RColorBrewer/index.html RColorBrewer [11].
- The http://code.google.com/p/bedtools/ BEDTools suite (
v2.15.0) [12], and the
http://xfer.curie.fr/get/nil/2Rpz9IfJKcZ/BEDTools_MapCount_ColorTag.tar.gz bamMapCount program to address common genomics tasks such as finding feature overlaps and grouping same features.
- The http://samtools.sourceforge.net/ SAMTools suite [10] to handle SAM and BAM format.
- The http://www.imagemagick.org/script/index.php Convert/ImageMagick utilies to format files and images.
- In order to use the end-user interface, a local server with php such as apache is needed.
- For Mac OS X user, make sure that you have http://developer.apple.com/xcode/ Xcode installed in your system.
Chongjian Chen
2012-01-26
