Answers.Body: <p>I have never used this tool before, but a simple search for it returns its <a href="https://ablab.github.io/spades/rna.html" rel="nofollow noreferrer">github page and documentation</a>. The files are explained in the relevant section:</p>
  <blockquote>
  <h3>rnaSPAdes output</h3>
  <p>rnaSPAdes outputs one main FASTA file named transcripts.fasta. The corresponding file with paths in the assembly_graph.fastg is transcripts.paths.</p>
  <p>In addition rnaSPAdes outputs transcripts with different level of filtration into /: - <code>hard_filtered_transcripts.fasta</code> - includes only long and reliable transcripts with rather high expression. - <code>soft_filtered_transcripts.fasta</code> - includes short and low-expressed transcripts, likely to contain junk sequences.</p>
  <p>We recommend using the main <code>transcripts.fasta</code> file in case you don't have any specific needs for your projects.</p>
  </blockquote>
  
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Answers.Text: Great! Thanks. Actually the same is also available in `Galaxy`. But the issue is that why is the number of sequences in `Transcripts` lower than `Soft-filtered transcripts` if they were "filtered"? Definately `Hard-filtered transcripts` should have the least number of sequences because it is "Hard Filtered". Maybe it has something to do deeper in the algorithm.
Answers.UserDisplayName: Eshaan IITM
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Answers.Text: @EshaanIITM Because "soft_filtered_transcripts.fasta - includes short and low-expressed transcripts, likely to contain junk sequences". So of course it has more. Don't look at the name, read the description in my answer. Everything is filtered somehow, including `Transcripts.fasta`. Then, you have the "soft" filtered, which is more inclusive and has more results, and the "hard" filtered which is more restrictive and has fewer.
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Answers.UserDisplayName: terdon
Body: <p>I'm running <code>RNASpades</code> for de-novo transcriptome assembly in the <code>Galaxy workflow manager</code></p>
  <p>. Instead of giving only one output of assembled Transcripts, it is giving three FASTA outputs namely:</p>
  <ol>
  <li><code>Transcripts</code> (37,741 sequences)</li>
  <li><code>Soft-filtered Transcripts</code> (46,250 sequences)</li>
  <li><code>Hard-filtered Transcripts</code> (29,808 sequences)</li>
  </ol>
  <p>Can I interpret that the <code>Transcripts</code> file represents some kind of optimization between <code>soft-filtered</code> and <code>hard-filtered transcripts</code>? if it helps, <code>RNASpades</code> selected two kmer values automatically when assembling the Transcripts.</p>
  
Tags: <rna-seq><assembly><transcriptome><galaxy>
Title: Why is RNASpades giving three FASTA output files instead of only one?
ThreadText: # Why is RNASpades giving three FASTA output files instead of only one?
  
  (Asked by: username_0 on 2024-07-13)
  
  I'm running `RNASpades` for de-novo transcriptome assembly in the `Galaxy workflow manager`
  
  . Instead of giving only one output of assembled Transcripts, it is giving three FASTA outputs namely:
  
  1. `Transcripts` (37,741 sequences)
  2. `Soft-filtered Transcripts` (46,250 sequences)
  3. `Hard-filtered Transcripts` (29,808 sequences)
  
  Can I interpret that the `Transcripts` file represents some kind of optimization between `soft-filtered` and `hard-filtered transcripts`? if it helps, `RNASpades` selected two kmer values automatically when assembling the Transcripts.
  
  **Tags:** rna-seq, assembly, transcriptome, galaxy
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2024-07-14. Score: 2
  
  I have never used this tool before, but a simple search for it returns its [github page and documentation](https://ablab.github.io/spades/rna.html). The files are explained in the relevant section:
  
  > ### rnaSPAdes output
  >
  > rnaSPAdes outputs one main FASTA file named transcripts.fasta. The corresponding file with paths in the assembly\_graph.fastg is transcripts.paths.
  >
  > In addition rnaSPAdes outputs transcripts with different level of filtration into /: - `hard_filtered_transcripts.fasta` - includes only long and reliable transcripts with rather high expression. - `soft_filtered_transcripts.fasta` - includes short and low-expressed transcripts, likely to contain junk sequences.
  >
  > We recommend using the main `transcripts.fasta` file in case you don't have any specific needs for your projects.
  
  > **Comments:**
  > **username_0**: Great! Thanks. Actually the same is also available in `Galaxy`. But the issue is that why is the number of sequences in `Transcripts` lower than `Soft-filtered transcripts` if they were "filtered"? Definately `Hard-filtered transcripts` should have the least number of sequences because it is "Hard Filtered". Maybe it has something to do deeper in the algorithm.  
  > **username_1**: @username_0 Because "soft_filtered_transcripts.fasta - includes short and low-expressed transcripts, likely to contain junk sequences". So of course it has more. Don't look at the name, read the description in my answer. Everything is filtered somehow, including `Transcripts.fasta`. Then, you have the "soft" filtered, which is more inclusive and has more results, and the "hard" filtered which is more restrictive and has fewer.  
  
  ---
  
  