03-02-2015
updates:
03/02/2015:
1, more work on the concept map:
will use bowtie2 to map the sRNAs sequences to the col-O genome sequence;
will use cufflinks2 to calculate how many reads are mapped within a gene.
both bowtie2 and cufflinks2 apps are available in iPlant.
2, input/output:
sRNAs sequence profile:
GSE62801: flowers
Col0 replicate 1 small RNA |
|
Col0 replicate 2 small RNA |
|
Col0 replicate 3 small RNA |
dcl3 replicate 1 small RNA |
|
dcl3 replicate 2 small RNA |
|
dcl3 replicate 3 small RNA |
GSE14695:
GSM366868 Whole-aerial_Col-0
GSM366870 Whole-aerial_dcl2-1dcl3-1dcl4-2
col-0 genome sequence and annotation file are needed.
QUESTION: which file format should be used in iplant/bowtie2?
FTP/HTTP means? .txt gz.
how to input the data into the iPLANT?
How much room do we have ?
bowtie2:
input:
reference col-0 genome sequence: fasta;
query sRNAs sequences: short reads /fastq/fasta/csfastq;
output:
SAM format;
Transform SAM format to BAM format for cufflinks.
cufflinks:
input: sorted.BAM+annotation.gtf;
output: transcripts.gtf (sRNAs.gtf).
FPKM: Fragments Per Kilobase of exon per Million fragments mapped.
future tasks:
download all sequence files;
try bowtie2 in iPLANT.