Extract transcripts - TSI
Version 1

Workflow Type: Galaxy

This is part of a series of workflows to annotate a genome, tagged with TSI-annotation. These workflows are based on command-line code by Luke Silver, converted into Galaxy Australia workflows.

The workflows can be run in this order:

  • Repeat masking
  • RNAseq QC and read trimming
  • Find transcripts
  • Combine transcripts
  • Extract transcripts
  • Convert formats
  • Fgenesh annotation

About this workflow:

  • Input: merged_transcriptomes.fasta.
  • Runs TransDecoder to produce longest_transcripts.fasta
  • (Runs both the LongOrfs and Predict parts together. Default settings except Long Orfs options: -m =20)
  • Runs Busco on output.

Inputs

ID Name Description Type
merged_transcriptomes.fasta #main/merged_transcriptomes.fasta n/a
  • File

Steps

ID Name Description
1 Text transformation toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/9.3+galaxy1
2 TransDecoder toolshed.g2.bx.psu.edu/repos/iuc/transdecoder/transdecoder/5.5.0+galaxy2
3 Busco toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.5.0+galaxy0

Outputs

ID Name Description Type
busco_sum #main/busco_sum n/a
  • File
busco_table #main/busco_table n/a
  • File
out_bed #main/out_bed n/a
  • File
out_cds #main/out_cds n/a
  • File
out_gff3 #main/out_gff3 n/a
  • File
out_lo_cds #main/out_lo_cds n/a
  • File
out_lo_pep #main/out_lo_pep n/a
  • File
out_pep #main/out_pep n/a
  • File

Version History

Version 1 (earliest) Created 8th May 2024 at 08:15 by Anna Syme

Initial commit


Frozen Version-1 3372155
help Creators and Submitter
Creators
Submitter
Citation
Silver, L., & Syme, A. (2024). Extract transcripts - TSI. WorkflowHub. https://doi.org/10.48546/WORKFLOWHUB.WORKFLOW.879.1
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Views: 226

Created: 8th May 2024 at 08:15

Last updated: 9th May 2024 at 05:08

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Total size: 316 KB
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