TranscriptsAnnotation-i5only-wf
Version 1

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
help Creators and Submitter
Creators
  • Arnaud Meng
  • Maxim Scheremetjew
  • Michael Crusoe
Submitter
Activity

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

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