TranscriptsAnnotation-i5only-wf
Version 1

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Transcripts annotation workflow

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SEEK ID: https://dev.workflowhub.eu/workflows/31?version=1

Inputs

ID Name Description Type
transcriptsFile n/a n/a
  • File
singleBestOnly n/a n/a
  • boolean?
replace n/a n/a
  • ../utils/esl-reformat-replace.yaml#replace?
diamondSeqdb n/a n/a
  • File
i5_chunk_size n/a n/a
  • int?
i5Databases n/a n/a
  • Directory
i5Applications n/a n/a
  • ../tools/InterProScan/InterProScan-apps.yaml#apps[]?
i5OutputFormat n/a n/a
  • ../tools/InterProScan/InterProScan-protein_formats.yaml#protein_formats[]?
blockSize n/a n/a
  • float?
covariance_models n/a n/a
  • File[]
clanInfoFile n/a n/a
  • File
cmsearchCores n/a n/a
  • int
buscoMode n/a n/a
  • ../tools/BUSCO/BUSCO-assessment_modes.yaml#assessment_modes
buscoOutputName n/a n/a
  • string
buscoLineage n/a n/a
  • Directory

Steps

ID Name Description
cut_fasta_header Cuts FASTA headers which are too long n/a
clean_fasta_header Replaces problematic characters from FASTA headers with dashes n/a
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_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
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

Version History

Version 1 (earliest) Created 25th Feb 2020 at 13:18 by Finn Bacall

Added/updated 26 files


Open master 41d0b78
help Creators and Submitter
Creators
Not specified
Additional credit

Arnaud Meng, Maxim Scheremetjew, Michael Crusoe

Submitter
License
Apache License 2.0
Activity

Views: 1626   Downloads: 288

Created: 25th Feb 2020 at 13:18

Last updated: 25th Feb 2020 at 15:17

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