03-23-2015

Owned by wenchen
Last updated: Mar 24, 2015Version comment
1 min read

Done:

    Use Bowtie2 to map the sRNAs in dcl3 or_ dcl2 dcl3 dcl4_ to the genomic DNA of col-0:

    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.

Result sample:

    Tabular View:


   
BowtieOut.sam:

Problems:

Can we load multiple query files (such as files in the same folder) in one analysis when using bowtie2?

Plan: 

    1, Transform SAM format to BAM format for using cufflinks;

loadexperiment cogepedia  fastq data

    2, Try to use cufflinks2 to calculate the sRNAs levels within each locus.