If you are following the transcript annotation workflow (i.e., if you chose Transcriptome/RNA-Seq Assembly in the Choose Assembly Workflow screen, and de novo assembly in the Choose Assembly Type screen), output results are saved in a folder called [project name] De Novo Transcriptome Assembly. This folder contains the following subfolders and files:
Subfolder |
File/Folder Name |
Description | ||||||||||||||||||||||||||||||||||||||
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[project name]_rnaAssemble.script |
Input script used to create the assembly results. This file can be opened in SeqMan Pro in order to examine isoforms using the Feature Table. | ||||||||||||||||||||||||||||||||||||||
Assemblies |
[project name]_novel_transcripts.sqd |
SQD assembly of all contigs that did not have a database match. | ||||||||||||||||||||||||||||||||||||||
[project name]_unassembled.fastq |
Multi-sequence FASTQ file with all unclustered and unassembled sequences. | |||||||||||||||||||||||||||||||||||||||
sub_0 (folder)k |
Folder containing sub-folders (sub_0, sub_1, etc.) with a separate .sqd document for each final assembly. If available, gene and organism names are used to create the file names. | |||||||||||||||||||||||||||||||||||||||
Intermediate Assembly Results |
cluster (folder) |
Intermediate results are deleted by default at the end of the assembly, but can be retained by setting the input script parameter deleteIntermediate to ‘false.’ | ||||||||||||||||||||||||||||||||||||||
combine (folder) | ||||||||||||||||||||||||||||||||||||||||
intermediateFiles (folder) | ||||||||||||||||||||||||||||||||||||||||
Reports |
[project name].AllTranscripts.SearchResults.txt |
Excel file containing summary information for each of the final assembled contigs. The table automatically opens for viewing when you open a .Transcriptome package in SeqMan Pro. The table, known in SeqMan Pro as the “All Transcripts” table, contains the following columns:
*Custom columns: These four columns use default names (e.g., Gene name, Organism name) if one of the default RefSeq databases was used in the SeqMan NGen assembly. However, if you used a custom GREP expression or a custom database that did not include these fields, these columns may have different names or be absent from the table. | ||||||||||||||||||||||||||||||||||||||
[project name].AllTranscripts.Table.txt |
Excel file containing summary information for each of the final assembled contigs. The table contains the following columns:
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Transcripts |
[project name]_identified_transcripts.fas |
Multi-sequence .fasta file containing the consensus sequences from all the assembled contigs that had a database match. Header lines for each entry contain the name and sequence length. | ||||||||||||||||||||||||||||||||||||||
[project name]_novel_transcripts.fas |
Multi-sequence .fasta file containing the consensus sequences from all the assembled contigs that did not have a database match. Header lines for each entry contain the name and sequence length. |