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Genomes
Genomes
 
 
Others
Others
 
 
PE RNA-Seq
PE RNA-Seq
 
 
SAT
SAT
 
 
SE RNA-Seq
SE RNA-Seq
 
 
Transcripts
Transcripts
 
 
README.md
README.md
 
 

README.md

SE RNA-Seq

  • Eight single-end RNA-Seq datasets (SRR2144382.fastq.zip, SRR2144383.fastq.zip, SRR2144384.fastq.zip, SRR2144385.fastq.zip, SRR2144410.fastq.zip, SRR2144411.fastq.zip, SRR2144442.fastq.zip, SRR2144443.fastq.zip)
  • DE_Info: A semicolon seperated matrix containing used for identifying differential expression transcripts.
  • mapping_info: RNA-Seq information for aligning reads to reference genome.

PE RNA-Seq

  • Eight paired-end RNA-Seq datasets (ERR712354_1.fastq.zip, ERR712354_2.fastq.zip; ERR712365_1.fastq.zip, ERR712365_2.fastq.zip; SRR445245_1.fastq.zip, SRR445245_2.fastq.zip; SRR445382_1.fastq.zip, SRR445382_2.fastq.zip; SRR1765337_1.fastq.zip, SRR1765337_2.fastq.zip; SRR1765338_1.fastq.zip, SRR1765338_2.fastq.zip; SRR1765379_1.fastq.zip, SRR1765379_2.fastq.zip; SRR1765380_1.fastq.zip, SRR1765380_2.fastq.zip)
  • mapping_info: RNA-Seq information for aligning reads to reference genome.

Genomes

This folder includes three demo of reference genomes (maize.fa.zip, Oryza.fa.zip, Sorghum.fa.zip) and an annotation of maize genomes (maize.gff3.zip).

Transcripts

This folder includes two well-annotated transcripts ("ref_trans.fasta.zip", "ref_trans_1.fasta.zip").

SAT

This folder includes four files of sequences (negative_cds.fa, negative_cds.fa_BG.fa, positive_cds.fa, positive_cds.fa_BG.fa, test_cds.fa).

Others

This folder includes seven files (Assembled_transcript.fasta, Assembled_transcript_expression, AS_test.gtf.zip, Cont_seq.fasta, Differentially_expressed_transcript_expression, RNA-Seq_sample_information, Batch_information.zip).

For each function:

  • (1) Quality Control

    This function needs a file or a collection of RNA-Seq. User can use RNA-Seq data in the folder "SE RNA-Seq".

  • (2) Trim Raw Reads

    The test data for this function include a collection of RNA-Seq from the folder "SE RNA-Seq". (upload as a collection, SEE USER MANNUAL)

    (The data which are in "PE RNA-Seq" can be also applied in this function.)

  • (3) Extract Unmapped Reads

    The test data for this function include "maize.fa.zip" from the folder "Genomes", and trimmed RNA-Seq data generated from the function "Trim Raw Reads".

  • (4) Remove Contamination

    This function needs these test data:

    1) Unmapped reads generated from the function "Extract Unmapped Reads";
2) Contamination sequence: "Cont_seq.fasta" from the folder "others";

  • (5) Assemble Unmapped Reads

    The test data for this function is unmapped reads from the function either "Extract Unmapped Reads" or "Remove Contamination".

  • (6) Expression-level Evidence

    This function needs the assembled transcripts generated from the function "Assemble Unmapped Reads".

  • (7) Genome-level Evidence

    This function needs reference genomes from the folder "Genomes" (upload as a collection), and "Assembled_transcript.fasta" from the folder "others".

  • (8) Transcript-level Evidence

    This function needs well-annotated transcripts from the folder "Transcripts" (upload as a collection), and "Assembled_transcript.fasta" from the folder "others".

  • (9) Protein-level Evidence

    This function needs the assembled transcripts generated from the function "Assemble Unmapped Reads".

  • (10) Species Assignment of Transcripts

    The test data for this function are in the folder "SAT".

  • (11) Characterize Nucleic-acid-based Features The test data for this function are "Assembled_transcript.fasta" from the folder "others", and a well-annotated transcripts (such as "ref_trans.fasta.zip") from the folder "Transcripts".

  • (12) Characterize Amino-acid-based Features The test data for this function are the same as the function "Characterize Nucleic-acid Feature"

  • (13) Detect Alternative Splicing Events

    This function needs the file "AS_test.gtf.zip" in the folder "others".

  • (14) Analysis of Condition Specificity

    This function needs the file "Assembled_transcript_expression", and "RNA-Seq_sample_information" in the folder "others".

  • (15) Heterogeneous Analysis

    This function needs the file "Assembled_transcript_expression" in the folder "others".

  • (16) Differential Expression Analysis

    This function needs the file "Assembled_transcript.fasta" in the folder "Others" and RNA-Seq data from the folder "RNA-Seq" (upload as a collection)

  • (17) Co-expression and Gene Ontology Enrichment Analysis

    This function needs the file "Differentially_expressed_transcript_expression".

  • (18) Extract Sequences

    This function needs the file "maize.fa.zip", "maize.gff3.zip" and "Assembled_transcript.fasta" in the folder "Others" and a transcript ID list generated from "Analyze Differential Expression".

  • (19) Remove Batch Effect

    This function needs the file "Assembled_transcript_expression", and "Batch_information.zip" in the folder "others".