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Wen's Program

Wen's Program

Mar 24, 2015

Programs:

1, Bowtie2: 

    Use Bowtie2 to map the sRNAs in dcl3 or dcl2 dcl3 dcl4 to the genomic DNA of col-0.

    We use Bowtie2 in the iPlant through the following steps:

    1, download and install the virtualbox for windows and CentOS-6.3-x86 in windows system;

    2, in CentOS-6.3-x86, download the sRNAs profile files (.fastq files) from GEO, and download the sequence files of each chromatin of col-0 (.fas files). Formats are required by bowtie2;

    3, download and install iCOMMANDS according to the introduction in https://pods.iplantcollaborative.org/wiki/display/DS/Using+iCommands;

    4, in the terminal, connect to the iPlant by icommand: $iinit;

    5, use icommands to enter the target folds in iPlant, and upload files through $iput;

    6, use command lines to aggregate the chromatin files into a single filecol-0_whole_geonme.fas. For example: $cat TAIR10_chr1.fas >>col-0_whole_geonme.fas;

    7, upload the whole genome file into iPlant, using $iput;

    8, in iPlant discovery environment, run bowtie-2.2.1--Build_and_Map, with one query file in every analysis.

2, cufflink: