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.
DESeq: R パッケージのDESeqを用いてサンプル間で発現量に変化があるものを抽出します。

Multi samples analysis

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

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.

Results of in line control

Sample name	Reads	Mapped to control	Ratio
HT_0	9,588,131	0	0 ppm
HT_140	10,948,077	0	0 ppm
HT_250	13,677,874	0	0 ppm
HT_500	7,884,258	0	0 ppm