Transcripts annotation workflow
Inputs
ID | Name | Description | Type |
---|---|---|---|
transcriptsFile | n/a | n/a | File |
singleBestOnly | n/a | n/a | n/a |
replace | n/a | n/a | n/a |
diamondSeqdb | n/a | n/a | n/a |
i5_chunk_size | n/a | n/a | int? |
i5Databases | n/a | n/a | n/a |
i5Applications | n/a | n/a | n/a |
i5OutputFormat | n/a | n/a | n/a |
blockSize | n/a | n/a | n/a |
covariance_models | n/a | n/a | n/a |
clanInfoFile | n/a | n/a | n/a |
cmsearchCores | n/a | n/a | n/a |
buscoMode | n/a | n/a | n/a |
buscoOutputName | n/a | n/a | n/a |
buscoLineage | n/a | n/a | n/a |
Steps
ID | Name | Description |
---|---|---|
cut_fasta_header | Cuts FASTA headers which are too long | |
clean_fasta_header | Replaces problematic characters from FASTA headers with dashes | |
identify_coding_regions | Identifies candidate coding regions within transcript sequences | |
remove_asterisks_and_reformat | Removes asterisks characters from given peptide sequences | |
functional_analysis | Matches are generated against predicted CDS, using a sub set of databases from InterPro. | |
calculate_diamond_matches | Calculates Diamond matches | |
identify_nc_rna | Identifies non-coding RNAs using Rfams covariance models | |
run_transcriptome_assessment | Performs transcriptome assessment using BUSCO |
Outputs
ID | Name | Description | Type |
---|---|---|---|
cutted_transcripts_file | n/a | n/a | File |
cleaned_transcripts_file | n/a | n/a | File |
peptide_sequences | n/a | n/a | File |
coding_regions | n/a | n/a | File |
gff3_output | n/a | n/a | File |
bed_output | n/a | n/a | File |
reformatted_sequences | n/a | n/a | File |
i5Annotations | n/a | n/a | File |
diamond_matches | n/a | n/a | File |
deoverlapped_matches | n/a | n/a | File |
busco_short_summary | n/a | n/a | File |
busco_full_table | n/a | n/a | File |
busco_missing_buscos | n/a | n/a | File |
busco_hmmer_output | n/a | n/a | Directory |
busco_translated_proteins | n/a | n/a | Directory |
busco_blast_output | n/a | n/a | Directory |

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Views: 221 Downloads: 7
Created: 25th Feb 2020 at 13:18
Last updated: 25th Feb 2020 at 15:17
Last used: 17th Jan 2021 at 20:32

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Version History
Version 1 Created 25th Feb 2020 at 13:18 by Finn Bacall
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