Workflow Type: Common Workflow Language
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Transcripts annotation workflow
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Inputs
ID | Name | Description | Type |
---|---|---|---|
transcriptsFile | n/a | n/a |
|
singleBestOnly | n/a | n/a |
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replace | n/a | n/a |
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phmmerSeqdb | n/a | n/a |
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diamondSeqdb | n/a | n/a |
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i5Databases | n/a | n/a |
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i5Applications | n/a | n/a |
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i5OutputFormat | n/a | n/a |
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blockSize | n/a | n/a |
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covariance_models | n/a | n/a |
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clanInfoFile | n/a | n/a |
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cmsearchCores | n/a | n/a |
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buscoMode | n/a | n/a |
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buscoOutputName | n/a | n/a |
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buscoLineage | n/a | n/a |
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Steps
ID | Name | Description |
---|---|---|
identify_coding_regions | Identifies candidate coding regions within transcript sequences | n/a |
remove_asterisks_and_reformat | Removes asterisks characters from given peptide sequences | n/a |
functional_analysis | n/a | Matches are generated against predicted CDS, using a sub set of databases from InterPro. |
calculate_phmmer_matches | Calculates phmmer matches | n/a |
calculate_diamond_matches | Calculates Diamond matches | n/a |
identify_nc_rna | Identifies non-coding RNAs using Rfams covariance models | n/a |
run_transcriptome_assessment | Performs transcriptome assessment using BUSCO | n/a |
Outputs
ID | Name | Description | Type |
---|---|---|---|
peptide_sequences | n/a | n/a |
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coding_regions | n/a | n/a |
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gff3_output | n/a | n/a |
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bed_output | n/a | n/a |
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reformatted_sequences | n/a | n/a |
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i5Annotations | n/a | n/a |
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phmmer_matches | n/a | n/a |
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diamond_matches | n/a | n/a |
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deoverlapped_matches | n/a | n/a |
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busco_short_summary | n/a | n/a |
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busco_full_table | n/a | n/a |
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busco_missing_buscos | n/a | n/a |
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busco_hmmer_output | n/a | n/a |
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busco_translated_proteins | n/a | n/a |
|
busco_blast_output | n/a | n/a |
|
Version History
Version 1 (earliest) Created 25th Feb 2020 at 13:19 by Finn Bacall
Added/updated 25 files
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Views: 1647 Downloads: 245
Created: 25th Feb 2020 at 13:19
Last updated: 25th Feb 2020 at 16:06
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