Edta summary output

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1

Could you please also add EDTA summary file in the EDTA output.

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2

Hi @Arslan_Tariq

Yes, we can make a request for updates to existing tools but I’m wondering if modifying the usage might help instead?

Is this the tool?

If that is correct, the tool form has some usage help. Please review and let us know what you think.

Help

Outputs

  1. A non-redundant TE library. The curated library will be included in this file if provided. TEs are classified into the superfamily level and using the three-letter naming system reported in Wicker et al. (2007).(A unified classification system for eukaryotic transposable elements | Nature Reviews Genetics). Each sequence can be considered as a TE family.

Optional

  1. Novel TE families: This file contains TE sequences that are not included in the curated library (curatedlib required).
  2. Whole-genome TE annotation: This file contains both structurally intact and fragmented TE annotations (anno required).
  3. Summary of whole-genome TE annotation: (anno required).
  4. Low-threshold TE masking: This is a genome file with only long TEs (>=1 kb) being masked. You may use this for de novo gene annotations. In practice, this approach will reduce overmasking for genic regions, which can improve gene prediction quality. However, initial gene models should contain TEs and need further filtering (anno required).
  5. Annotation inconsistency for simple TEs: (anno and evaluate required).
  6. Annotation inconsistency for nested TEs: (anno and evaluate required).
  7. Overall annotation inconsistency: (anno and evaluate required).

Tool form options referenced

Curated Library File - optional

Provided a curated library to keep consistant naming and classification for known TEs. All TEs in this file will be trusted 100%, so please ONLY provide MANUALLY CURATED ones here. (–curatedlib)

Would you like to perform whole-genome TE annotation after TE library construction?

Perform or not perform whole-genome TE annotation after TE library construction. (–a)

Evaluate

Evaluate (1) classification consistency of the TE annotation (–evaluate)

The option is named as --anno in the help but this is the same as the --a option on the form (truncated, maybe a bit confusing!). If your goal is to output the 3 summary, then you’ll want to use this option.

  1. Summary of whole-genome TE annotation: (anno required).

Does this help to confirm the usage or do you want to follow up more? Would you like to share your example? Screenshots of the job Details view (showing the table of inputs/parameters and the outputs) or a shared history link (contains everything) would help to provide context. Or, am I guessing about the wrong tool form? Or, do you think there is a problem – do you currently have unexpected outputs?

Let’s start there! :slight_smile:

3

Thank you for your reply.

I tried with --a, but only getting three output files.

  • TE masked genome
  • TE library in fasta format
  • TE annotation in gff format

It is not producing any summary file.

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Here is the command:

ln -s '/data/dnb12/galaxy_db/files/f/3/e/dataset_f3ed13a5-b404-457a-94b0-8056b8af15fe.dat' ./input.fa && EDTA.pl --genome input.fa --species 'Others' --step 'all' --cds '/data/dnb12/galaxy_db/files/9/0/2/dataset_9027727a-c3e5-432c-bbf1-6c2ef72035ac.dat' --sensitive 1 --anno 1  &&  mv ./input.fa.mod.EDTA.anno/*.sum .