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.

Project settings

Project name	The project name would be used for the URL (/pothos/project_name/) and the prefix of the contig name (project_name000001.000).Only alphabet is allowed. The short words expressing the organism (exp: Arabidopsis thaliana -> Ath) was recomended.
Scientific name or nickname	Please input the scientific name or nickname for the subject of your research project. You can input alphabet, number and symbols (.-_#).
Correspondence	Please input your name (Ex: John Smith).
e-mail address	The mail would be sent to this address at the end of calculation.
Appearance	Select appearance of project.
Limitation for browsing	You can limit the users who could browse this project.
Limitation for editing	You can limit the users who could configure the analysis settings.