text: user1684: I did RNA-seq of mammalian cells infected with pox virus. Now, I have read files which contain both host and virus reads. I want to align the reads both to host and viral genome. I was thinking I could concatenate the host and virus genome into one file and run Salmon against this concatenated genome.
  However, salmon recommends transcriptome file for assembly which are not available for viruses. Virus genome are available as GenBank or GFF3 format from NCBI. Is there any way I can concatenate these formats into the format that can be used by salmon? Or is there any way around to use virus genome as reference in salmon?
  
  Citing the website:
  Salmon is a tool for quantifying the expression of transcripts using RNA-seq data. Salmon uses new algorithms (specifically, coupling the concept of quasi-mapping with a two-phase inference procedure) to provide accurate expression estimates very quickly (i.e. wicked-fast) and while using little memory.
  Patro, R., Duggal, G., Love, M. I., Irizarry, R. A., & Kingsford, C. (2017). Salmon provides fast and bias-aware quantification of transcript expression. Nature Methods.
  
  user383: You provide Salmon with a transcriptome fasta... so merging the human transcriptome with the pox virus genome fasta file should work. You don't mention that in your post but the viral genome should exist as a fasta. You can extract the sequences from genbank or maybe you can find our virus here: https://www.ebi.ac.uk/genomes/virus.html
  You can find the coding transcriptome at the link below in the cdna folder.
  The non-coding transcriptome is in the ncrna. You should probably merge them:
  ftp://ftp.ensembl.org/pub/release-95/fasta/homo_sapiens/
  
original_text: 1684: <p>I did RNA-seq of mammalian cells infected with pox virus. Now, I have read files which contain both host and virus reads. I want to align the reads both to host and viral genome. I was thinking I could concatenate the host and virus genome into one file and run <a href="https://combine-lab.github.io/salmon/" rel="nofollow noreferrer">Salmon</a> against this concatenated genome.</p>
  <p>However, salmon recommends transcriptome file for assembly which are not available for viruses. Virus genome are available as GenBank or GFF3 format from NCBI. Is there any way I can concatenate these formats into the format that can be used by salmon? Or is there any way around to use virus genome as reference in salmon?</p>
  <hr />
  <p>Citing the website:</p>
  <p>Salmon is a tool for quantifying the expression of transcripts using RNA-seq data. Salmon uses new algorithms (specifically, coupling the concept of quasi-mapping with a two-phase inference procedure) to provide accurate expression estimates very quickly (i.e. wicked-fast) and while using little memory.</p>
  <p>Patro, R., Duggal, G., Love, M. I., Irizarry, R. A., &amp; Kingsford, C. (2017). Salmon provides fast and bias-aware quantification of transcript expression. Nature Methods.</p>
   383: <p>You provide Salmon with a transcriptome fasta... so merging the human transcriptome with the pox virus genome fasta file should work. You don't mention that in your post but the viral genome should exist as a fasta. You can extract the sequences from genbank or maybe you can find our virus here: <a href="https://www.ebi.ac.uk/genomes/virus.html" rel="nofollow noreferrer">https://www.ebi.ac.uk/genomes/virus.html</a></p>
  
  <p>You can find the coding transcriptome at the link below in the <strong>cdna</strong> folder.
  The non-coding transcriptome is in the <strong>ncrna</strong>. You should probably merge them:</p>
  
  <p><a href="ftp://ftp.ensembl.org/pub/release-95/fasta/homo_sapiens/" rel="nofollow noreferrer">ftp://ftp.ensembl.org/pub/release-95/fasta/homo_sapiens/</a></p>
  