<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>

CC BY-SA 4.0
2024-07-15T11:21:37.353Z
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.
Eshaan IITM
CC BY-SA 4.0
2024-07-15T11:28:50.133Z
@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.
terdon
CC BY-SA 4.0
2024-07-14T17:36:06.263Z
2024-07-14T20:53:37.270Z
2024-07-14T20:53:37.270Z
terdon
<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>

<rna-seq><assembly><transcriptome><galaxy>
Why is RNASpades giving three FASTA output files instead of only one?
# 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

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## 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**: @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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