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.

Start annotation

Please configure the annotation process. The first step of annotation process is to find homologous sequence from database by BLAST. Plase select database and set the threshold value for e-value. The BLASE search will be done from top to bottom of list. If you check, the BLAST search will be done for the unannotated sequences.

Database as referencee-value