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.

Result of assemble

Reads (1)	38,073,218
Reads (2)	31,848,082
Number of contig	53,516
Whole length of contings	63,096,852 bp
Mean length of contigs	1,179 bp
Median length of contigs	803 bp
Maximum length of contigs	16,785 bp
Minimum length of contigs	201 bp
N50 of contigs	1,919 bp
N90 of contigs	518 bp

Histgram of length of contigs

Download all assembled sequence