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.