Answers.Body: <p>Pseudoaligmnent to a reference transcriptome with something like Kallisto is perfectly valid, assuming you are in an organism whose reference transcriptome is very well documented.</p>
  <p>But if you want to find novel transcripts or novel splicing junctions, you need to align to genome.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-08-05T20:57:25.183Z
Answers.Text: thank you! Could I use STAR or a similar program (not Kallisto or Salmon etc) with reference transcriptome?
Answers.UserDisplayName: marilu
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Answers.CreationDate: 2020-08-05T21:07:57.403Z
Answers.Text: You can make a STAR reference out of a transcriptome, but why would you do that?  It wasn't designed to be run like that.
Answers.UserDisplayName: swbarnes2
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Answers.CreationDate: 2020-08-05T21:24:47.043Z
Answers.Text: if i am only interested in differential expression, could i use star with reference transcriptome to decrease computational effort?
Answers.UserDisplayName: marilu
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Answers.CreationDate: 2020-08-05T21:34:07.170Z
Answers.Text: As a rule, do not use programs for things they were not designed for unless you are absolutely sure you understand what you are doing and why.  If you want something faster than STAR, use Kallisto.
Answers.UserDisplayName: swbarnes2
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Answers.CreationDate: 2020-08-05T21:36:05.487Z
Answers.Text: I actually think you could run STAR on a transcriptome. In their manuscript, you can run alignment using a GTF file.
Answers.UserDisplayName: Phoenix Mu
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Answers.CreationDate: 2020-08-05T21:38:28.947Z
Answers.Text: I didn't say you couldn't, just that there's no good reason to.  The point of a GTF file is to mark features, especially exons,  in a large genome, so there's little point in using one on a transcriptome.  And of course you can't align to a GTF alone.
Answers.UserDisplayName: swbarnes2
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Answers.CreationDate: 2020-08-06T10:02:36.493Z
Answers.Text: I'm confused, the GTF file *is* the reference transcriptome no? And the FASTA file the reference genome (of course both are needed to map to transcriptome)
Answers.UserDisplayName: Chris_Rands
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Answers.Text: @Chris_Rands I wouldn't have spontaneously called a GTF file a transcriptome. For me, a transcriptome would rather be a set of sequences (the sequences of the potential transcripts). But maybe this is not the common usage.
Answers.UserDisplayName: bli
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Answers.CreationDate: 2020-08-06T15:20:18.867Z
Answers.Text: @bli I agree, the transcriptome is maybe a set of mRNAs and not simply a tabular file format of course, but I was thinking in terms of how this information is stored
Answers.UserDisplayName: Chris_Rands
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Answers.CreationDate: 2020-08-07T08:59:43.543Z
Answers.Text: @Chris_Rands I never worked with a transcriptome, but I imagined that this was stored in the form of a fasta file containing all possible transcripts. And I imagined that mapping on a transcriptome was done via an index built on this fasta file. Is it actually more common to map on a genome and then infer transcripts based on information present in a GTF file?
Answers.UserDisplayName: bli
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Answers.Text: @bli i think splice aware aligners need the full genome FASTA but others use transcripts FASTA
Answers.UserDisplayName: Chris_Rands
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Body: <p>I would like to ask why in RNA seq analysis (alignment step) we use sometimes reference genome instead of reference transcriptome? thank you!</p>
  
Tags: <rna-seq><phylogenetics>
Title: why in RNA seq don't we only use reference transcriptome?
ThreadText: # why in RNA seq don't we only use reference transcriptome?
  
  (Asked by: username_0 on 2020-08-05)
  
  I would like to ask why in RNA seq analysis (alignment step) we use sometimes reference genome instead of reference transcriptome? thank you!
  
  **Tags:** rna-seq, phylogenetics
  
  
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  ## 1 answers
  
  ### Answer by username_1 on 2020-08-05. Score: 7
  
  Pseudoaligmnent to a reference transcriptome with something like Kallisto is perfectly valid, assuming you are in an organism whose reference transcriptome is very well documented.
  
  But if you want to find novel transcripts or novel splicing junctions, you need to align to genome.
  
  > **Comments:**
  > **username_0**: thank you! Could I use STAR or a similar program (not Kallisto or Salmon etc) with reference transcriptome?  
  > **username_1**: You can make a STAR reference out of a transcriptome, but why would you do that?  It wasn't designed to be run like that.  
  > **username_0**: if i am only interested in differential expression, could i use star with reference transcriptome to decrease computational effort?  
  > **username_1**: As a rule, do not use programs for things they were not designed for unless you are absolutely sure you understand what you are doing and why.  If you want something faster than STAR, use Kallisto.  
  > **username_2**: I actually think you could run STAR on a transcriptome. In their manuscript, you can run alignment using a GTF file.  
  > **username_1**: I didn't say you couldn't, just that there's no good reason to.  The point of a GTF file is to mark features, especially exons,  in a large genome, so there's little point in using one on a transcriptome.  And of course you can't align to a GTF alone.  
  > **username_3**: I'm confused, the GTF file *is* the reference transcriptome no? And the FASTA file the reference genome (of course both are needed to map to transcriptome)  
  > **username_4**: @username_3 I wouldn't have spontaneously called a GTF file a transcriptome. For me, a transcriptome would rather be a set of sequences (the sequences of the potential transcripts). But maybe this is not the common usage.  
  > **username_3**: @username_4 I agree, the transcriptome is maybe a set of mRNAs and not simply a tabular file format of course, but I was thinking in terms of how this information is stored  
  > **username_4**: @username_3 I never worked with a transcriptome, but I imagined that this was stored in the form of a fasta file containing all possible transcripts. And I imagined that mapping on a transcriptome was done via an index built on this fasta file. Is it actually more common to map on a genome and then infer transcripts based on information present in a GTF file?  
  > **username_3**: @username_4 i think splice aware aligners need the full genome FASTA but others use transcripts FASTA  
  
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