03-10-2015

Done:

1, download fasta files of col-0 genomic DNA sequence from TAIR:  

    TAIR10_chr1.fas, 

    TAIR10_chr2.fas, 

    TAIR10_chr3.fas, 

    TAIR10_chr4.fas, 

    TAIR10_chr5.fas,

    TAIR10_chrC.fas,

    TAIR10_chrM.fas.

2, download fastq files (required file format for bowtie2) of sRNAs in col-o, dcl3, and dcl2 dcl3 dcl4;

    GSE62801: flowers:

        3 repeats of col-0 sRNAs;

        3 repeats of dcl3 sRNAs.

    #GSE14695: whole aerial is replaced by GSE49866:

    GSE49866: flower:

        1 repeat of col-0 sRNAs;

        1 repeat of dcl2 dcl3 dcl4 sRNAs.

3, download annotation of col-0: 

    TAIR10_GFF3_genes_transposons.gff.

4, upload all the files into iPlant.

5, try bowtie2 in iPlant

future:

Finish the mapping by bowtie2.

Problems:

1, Should I include the chloroplast and mitochondrial DNA in the reference genome? Are those DNAs involved in the annotation file? Because otherwise I can not find out the locus of the sRNAs mapped to the chloroplast or mitochondrial DNA

   Or should I use the arabidopsis reference sequence involved in bowtie2? Is that version (enzemble 14) most updated?

2, when index the reference, only one file is allowed to be input. How can I make 7 files into 1?

3, iPlant keeps logging me out!!!

use iPlant command lines.

always try command.

google.