PoTHoS Phyto Transcriptomics by High-throughput Sequencer

Project

Top: Top page of project.
Settings: Configuration of project.
Register members: Control members who could access to data.

Sample

Register files: Submit fastq files (*.fastq.gz) for analysis.
Register samples: Group files into samples.
Register groups: Group samples.
系列登録: 登録したサンプルまたはグループを系列にします。
Quality of sample: Display the number of reads derived from the in-line control.

Assemble

Settings: Settings for the assembling of reads.
Result: Summary of the assemble.
Detail of contig: Display the sequence of contig.
Search contigs: Search contigs by using BLAST.
Detect SNPs: Display SNPs observed in contigs.

Annotation

Settings: Configure annotation options.
Result: Summary of Annotation.

Mapping

Settings: Settings for the mapping the reads to the assembled reference.
Summary of Mapping: Show the number of reads, rate for mapping by each sample.
Expression level: Show tag count for each contigs.
Display the mapped image (pile image): Draw pile image for the reads mapped to contig.

Two samples analysis

比較解析: サンプル間で発現量の比を計算し、遺伝子を絞り込みます。
Scatter plot: Draw scatter plot.

Multi samples analysis

Cluster analysis: Make a cluster of samples based on the expression pattern of contigs.

Two groups analysis

edgeR: Differentical analysis between two groups using edgeR, an R package.

Reference

Nucleotide sequences: Search transcript sequence.
Protein: Search amino acid sequence.
Genome: Show genome sequence.
Blast search: Search sequences registered in PoTHoS by BLAST.
キーワード検索: 配列IDまたはアノテーション中の文字列を検索します。
Download: Download nucleotide and amino acid sequences stored in PoTHoS as FASTA format.

Authentication

Login: Please login to show the data under access control.
Registration: Register e-mail address.

Summary of mapping.

Group	Sample name	Reads	Mapped reads	Ratio	reports	Ratio
x10m12h	x10m12h_1	7,191,686	6,115,899	85.0 %	0	0.0 %
x10m12h	x10m12h_2	6,724,218	5,996,322	89.2 %	0	0.0 %
x10m6h	x10m6h_1	7,762,282	7,142,267	92.0 %	0	0.0 %
x10m6h	x10m6h_2	12,988,857	11,988,841	92.3 %	0	0.0 %
x15m12h	x15m12h_1	8,496,774	7,848,310	92.4 %	0	0.0 %
	x15m12h_2	7,957,408	7,134,272	89.7 %	0	0.0 %
	x15m12h_3	5,541,018	4,807,498	86.8 %	0	0.0 %
	x15m12h_4	5,517,193	5,079,711	92.1 %	0	0.0 %
x15m6h	x15m6h_1	5,058,891	4,702,640	93.0 %	0	0.0 %
	x15m6h_2	11,288,307	10,287,160	91.1 %	0	0.0 %
	x15m6h_3	5,538,450	5,149,953	93.0 %	0	0.0 %
x5m12h	x5m12h_1	5,883,168	5,482,388	93.2 %	0	0.0 %
	x5m12h_2	6,301,956	5,740,435	91.1 %	0	0.0 %
	x5m12h_3	5,306,289	4,911,224	92.6 %	0	0.0 %
x5m6h	x5m6h_1	8,075,058	7,504,896	92.9 %	0	0.0 %
x5m6h	x5m6h_2	9,581,453	8,855,021	92.4 %	0	0.0 %
PG	xPG_1	11,291,155	10,601,254	93.9 %	0	0.0 %
	xPG_2	7,093,049	6,658,486	93.9 %	0	0.0 %
	xPG_3	6,898,284	6,468,936	93.8 %	0	0.0 %
	xPG_4	6,008,308	5,608,114	93.3 %	0	0.0 %
wo12h	xwo12h_1	5,641,268	5,084,301	90.1 %	0	0.0 %
	xwo12h_2	5,361,465	4,971,663	92.7 %	0	0.0 %
	xwo12h_3	1,125,659	1,026,341	91.2 %	0	0.0 %
wo6h	xwo6h_1	6,115,284	5,699,790	93.2 %	0	0.0 %
	xwo6h_2	1,112,684	1,021,749	91.8 %	0	0.0 %
	xwo6h_3	5,805,485	4,730,728	81.5 %	0	0.0 %
	xwo6h_4	407,577	361,441	88.7 %	0	0.0 %

Download tag count as CSV (2013/02/21 11:02 2013-02-21T11:02:37+09:00Thu, 21 Feb 2013 11:02:37 +0900Asia/Tokyoam28Asia/Tokyo21)

Download ppm of expression as CSV (2013/02/21 11:02 2013-02-21T11:02:38+09:00Thu, 21 Feb 2013 11:02:38 +0900Asia/Tokyoam28Asia/Tokyo21)