text: user6719: I'm studying on a plant that has no reference genome and only has one scaffold assembly and one gff3 annotation file. Can I create an index with the same assembly and gff3 in STAR and do the mapping? If I want to do de novo assembly using the Galaxy Can I import the links of 20 fastq files from the RNA-seq of the samples together to construct the Reference Genome with Trinity? If this is possible, please help me import the links of these files together into Galaxy and make the reference genome.
  Thanks a lot
  
  user3541: You have multiple questions, I will try to answer one by one:
  
  On creating an index with STAR: As long as you provide a fasta file and its corresponding gff, you will be able to generate an index.
  On creating a reference with Trinity: You have mentioned "to construct the Reference Genome with Trinity", however, with your RNA-seq data and Trinity, you can construct a de novo transcriptome and not a genome.
  Uploading files to Galaxy: I suggest to do so via FTP using FileZilla or something similar. The transfer can take some time if your files are large though.
  
  If I understand your questions correctly, you are performing RNA-seq and you are concerned about the completeness of the genome of your model organism. In that case, I would advise to bring together a de novo transcriptome from your RNA-seq data (with Trinity), use one of the quasi-mapping methods (with a tool like Salmon or kallisto).
  
original_text: 6719: <p>I'm studying on a plant that has no reference genome and only has one scaffold assembly and one gff3 annotation file. Can I create an index with the same assembly and gff3 in STAR and do the mapping? If I want to do de novo assembly using the Galaxy Can I import the links of 20 fastq files from the RNA-seq of the samples together to construct the Reference Genome with Trinity? If this is possible, please help me import the links of these files together into Galaxy and make the reference genome.</p>
  
  <p>Thanks a lot</p>
   3541: <p>You have multiple questions, I will try to answer one by one:</p>
  
  <ul>
  <li><p>On creating an index with <code>STAR</code>: As long as you provide a fasta file and its corresponding gff, you will be able to generate an index.</p></li>
  <li><p>On creating a reference with <code>Trinity</code>: You have mentioned "to construct the Reference Genome with Trinity", however, with your RNA-seq data and Trinity, you can construct a de novo transcriptome and not a genome.</p></li>
  <li><p>Uploading files to <code>Galaxy</code>: I suggest to do so via FTP using <code>FileZilla</code> or something similar. The transfer can take some time if your files are large though.</p></li>
  </ul>
  
  <p>If I understand your questions correctly, you are performing RNA-seq and you are concerned about the completeness of the genome of your model organism. In that case, I would advise to bring together a de novo transcriptome from your RNA-seq data (with Trinity), use one of the quasi-mapping methods (with a tool like <code>Salmon</code> or <code>kallisto</code>).</p>
  