Answers.Body: <p>You might be interested in the <a href="https://github.com/broadinstitute/catch#downloading-viral-sequence-data" rel="nofollow noreferrer">viral sequence data</a> from CATCH. There are various different viral subsets available.</p>
  <p>You could also try the NCBI virus website, filtering on human hosts. There's a &quot;Download&quot; link on this page that allows you to download the full sequence set:</p>
  <p><a href="https://www.ncbi.nlm.nih.gov/labs/virus/vssi/#/virus?VirusLineage_ss=Viruses,%20taxid:10239&amp;HostLineage_ss=humans,%20taxid:9605&amp;SeqType_s=Nucleotide" rel="nofollow noreferrer">https://www.ncbi.nlm.nih.gov/labs/virus/vssi/#/virus?VirusLineage_ss=Viruses,%20taxid:10239&amp;HostLineage_ss=humans,%20taxid:9605&amp;SeqType_s=Nucleotide</a></p>
  <p>You've asked a very specific question, so I'm giving you a very specific answer. It seems that what you <em>actually</em> want to do is different from the self-explanatory question.</p>
  <p>For the purpose of creating an index for Kallisto or Salmon, it should be okay to use the full dataset. Those programs are designed to handle eukaryotic transcriptomes as input, which typically include many gene copies and isoforms, so transcript / genome duplication shouldn't be much of an issue.</p>
  <p>Without knowing more about your particular application, it's difficult to provide additional advice. From what you've written, i.e. &quot;what proportion of my raw data is originated from virus RNA&quot;, a hit to <em>any</em> viral sequence would be sufficient. For example, if you want any more specific information about viral proportion / species, then you should be using a metagenomic tool like Kraken2, rather than Kallisto / Salmon.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-07-31T08:08:31.267Z
Answers.Text: Could you please explain this CATCH data more? Can I get cDNA of a specific virus in FASTA with annotated CDS?
  I already knew about NCBI virus database, the problem is that it doesn't tell you which genome/transcriptome is the reference one for many viruses and just gives you many different isolated strains. The second problem is that the FASTA file doesn't have separate head and sequence sections for each CDS in the virus genome but it has one head with all the sequences of the virus. So, I guess I can't use it for the quantification of viral transcripts with Kallisto. Am I wrong?
Answers.UserDisplayName: Reza Rezaei
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Answers.CreationDate: 2020-07-31T11:16:23.547Z
Answers.Text: Thanks @gringer this is a great answer. In fact it is a superb answer that I'll be following as well.
Answers.UserDisplayName: M__
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Answers.LastEditDate: 2020-08-02T01:01:15.190Z
Answers.UserDisplayName: gringer
Answers.Body: <p>I found a possible answer to my own question by reading this <a href="https://www.biostars.org/p/386742/" rel="nofollow noreferrer">biostar</a> page and also finding an NCBI page for downloading the reference genome file for viruses.</p>
  <ul>
  <li>You should go to this NCBI <a href="https://www.ncbi.nlm.nih.gov/genomes/GenomesGroup.cgi" rel="nofollow noreferrer">page</a> and search for your target virus.</li>
  <li>Then click on the virus name and you will be redirected to a page like <a href="https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?lvl=0&amp;id=11277" rel="nofollow noreferrer">this</a> which gives you an Entrez records table. You should click on the direct link in the genome row in the table.</li>
  <li>Click on <code>Genome Assembly and Annotation report </code> on the new page. You will be redirected to a page like <a href="https://www.ncbi.nlm.nih.gov/genome/browse/#!/viruses/4858/" rel="nofollow noreferrer">this</a> with some information on reference files submitted to NCBI. The last column in this table is for links to the NCBI FTP site. There are two options to access RefSeq or GenBank FTPs. You can choose either of them. I chose RefSeq. Then, you will be redirected to a page like <a href="ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/002/815/995/GCF_002815995.1_ASM281599v1" rel="nofollow noreferrer">this</a> with different fasta files for that specific virus.</li>
  <li>the file with the name <code>GCF_002815995.1_ASM281599v1_cds_from_genomic.fna.gz</code> is the transcriptome file annotated with CDS info which can be used for Kallisto alignment.</li>
  </ul>
  <p><strong>Note</strong>: If you couldn't find your desired virus genome in the NCBI page mentioned above, you can proceed with the method for generating your desired transcriptome file from genome and annotation file using <code>gffread</code> package. The details on this method are provided in the answer to the Biostar question mentioned above.</p>
  
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Answers.CreationDate: 2020-08-01T09:10:59.460Z
Answers.LastActivityDate: 2020-08-01T09:10:59.460Z
Answers.UserDisplayName: Reza Rezaei
Body: <p>I guess the title is self-explanatory. I'd like to find the reference transcriptome files for a few human viruses. My RNA-seq samples are from human tumor cells that were infected with viruses. The main part of my analysis is quantifying human gene expression from these samples. However, I also would like to find what proportion of my raw data is originated from virus RNA.</p>
  <p>So, I'd like to learn how to find the reference transcriptome data for human viruses. Moreover, I appreciate it if you could give me some insight into your workflow for approaching this problem. Finally, if there is any specific command line, R, or python tool for this specific task, I'd like to know about it.</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-07-30T21:37:56.967Z
Comments.Text: Interesting question, presume you're looking for things like HPV. Its a bit sparse on detail of course, so beyond a one word answer I'm not sure we can help. What about just using Blat?
Comments.UserDisplayName: M__
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-07-31T08:03:25.677Z
Comments.Text: @Michael HPV is a close example but my specific use case is for engineered viruses for cancer-killing. I mostly use VSV, VV, HSV, or Ad. What do you using Blat? Does it have a command-line interface? Can I give it raw fastq files? Does it give me the proportion of virus originated transcripts in my human transcript samples?
Comments.UserDisplayName: Reza Rezaei
Tags: <rna-seq><covid-19><sars-cov-2><kallisto><virus>
Title: How to get transcriptome FASTA file for viruses for Kallisto pseudo-alignment?
ThreadText: # How to get transcriptome FASTA file for viruses for Kallisto pseudo-alignment?
  
  (Asked by: username_0 on 2020-07-30)
  
  I guess the title is self-explanatory. I'd like to find the reference transcriptome files for a few human viruses. My RNA-seq samples are from human tumor cells that were infected with viruses. The main part of my analysis is quantifying human gene expression from these samples. However, I also would like to find what proportion of my raw data is originated from virus RNA.
  
  So, I'd like to learn how to find the reference transcriptome data for human viruses. Moreover, I appreciate it if you could give me some insight into your workflow for approaching this problem. Finally, if there is any specific command line, R, or python tool for this specific task, I'd like to know about it.
  
  **Tags:** rna-seq, covid-19, sars-cov-2, kallisto, virus
  
  > **Comments:**
  > **username_1**: Interesting question, presume you're looking for things like HPV. Its a bit sparse on detail of course, so beyond a one word answer I'm not sure we can help. What about just using Blat?  
  > **username_0**: @Michael HPV is a close example but my specific use case is for engineered viruses for cancer-killing. I mostly use VSV, VV, HSV, or Ad. What do you using Blat? Does it have a command-line interface? Can I give it raw fastq files? Does it give me the proportion of virus originated transcripts in my human transcript samples?  
  
  ---
  
  ## 2 answers
  
  ### Answer by username_2 on 2020-07-31. Score: 1
  
  You might be interested in the [viral sequence data](https://github.com/broadinstitute/catch#downloading-viral-sequence-data) from CATCH. There are various different viral subsets available.
  
  You could also try the NCBI virus website, filtering on human hosts. There's a "Download" link on this page that allows you to download the full sequence set:
  
  <https://www.ncbi.nlm.nih.gov/labs/virus/vssi/#/virus?VirusLineage_ss=Viruses,%20taxid:10239&HostLineage_ss=humans,%20taxid:9605&SeqType_s=Nucleotide>
  
  You've asked a very specific question, so I'm giving you a very specific answer. It seems that what you *actually* want to do is different from the self-explanatory question.
  
  For the purpose of creating an index for Kallisto or Salmon, it should be okay to use the full dataset. Those programs are designed to handle eukaryotic transcriptomes as input, which typically include many gene copies and isoforms, so transcript / genome duplication shouldn't be much of an issue.
  
  Without knowing more about your particular application, it's difficult to provide additional advice. From what you've written, i.e. "what proportion of my raw data is originated from virus RNA", a hit to *any* viral sequence would be sufficient. For example, if you want any more specific information about viral proportion / species, then you should be using a metagenomic tool like Kraken2, rather than Kallisto / Salmon.
  
  > **Comments:**
  > **username_0**: Could you please explain this CATCH data more? Can I get cDNA of a specific virus in FASTA with annotated CDS? I already knew about NCBI virus database, the problem is that it doesn't tell you which genome/transcriptome is the reference one for many viruses and just gives you many different isolated strains. The second problem is that the FASTA file doesn't have separate head and sequence sections for each CDS in the virus genome but it has one head with all the sequences of the virus. So, I guess I can't use it for the quantification of viral transcripts with Kallisto. Am I wrong?  
  > **username_1**: Thanks @username_2 this is a great answer. In fact it is a superb answer that I'll be following as well.  
  
  ---
  
  ### Answer by username_0 on 2020-08-01. Score: 1
  
  I found a possible answer to my own question by reading this [biostar](https://www.biostars.org/p/386742/) page and also finding an NCBI page for downloading the reference genome file for viruses.
  
  * You should go to this NCBI [page](https://www.ncbi.nlm.nih.gov/genomes/GenomesGroup.cgi) and search for your target virus.
  * Then click on the virus name and you will be redirected to a page like [this](https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?lvl=0&id=11277) which gives you an Entrez records table. You should click on the direct link in the genome row in the table.
  * Click on `Genome Assembly and Annotation report`  on the new page. You will be redirected to a page like [this](https://www.ncbi.nlm.nih.gov/genome/browse/#!/viruses/4858/) with some information on reference files submitted to NCBI. The last column in this table is for links to the NCBI FTP site. There are two options to access RefSeq or GenBank FTPs. You can choose either of them. I chose RefSeq. Then, you will be redirected to a page like [this](ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/002/815/995/GCF_002815995.1_ASM281599v1) with different fasta files for that specific virus.
  * the file with the name `GCF_002815995.1_ASM281599v1_cds_from_genomic.fna.gz` is the transcriptome file annotated with CDS info which can be used for Kallisto alignment.
  
  **Note**: If you couldn't find your desired virus genome in the NCBI page mentioned above, you can proceed with the method for generating your desired transcriptome file from genome and annotation file using `gffread` package. The details on this method are provided in the answer to the Biostar question mentioned above.
  
  
  ---
  
  