text: user15408: Forgive the basic question here, but I'm super novice at this ...
  I have a series of paired-end RNA fastq files (e.g. SRR10720226_1.fastq.gz and SRR10720226_2.fastq.gz).  I'm trying to figure out what software I need to use to translate those into proteins.
  I was trying to use biopython to do this using the translate method.  The problem is biopython doesn't seem to consider both files together, only one fastq at a time.
  Which tool should I use to work with the reads together?  Is there anything else I should be doing besides just translating to protein?
  
  user9497: This is a much more complicated question than it might seem.
  First, you need to understand how RNA-Seq works, and what your data really is. Your "paired-end files" contain reads, which will contain fragments of transcripts.
  Since those are only fragments of transcripts, you don't know what frame they are in, so you don't have a single possible translation. And each read would only give you a small part of the protein.
  Since the data is for humans, your best course of action would be to first, align the reads to the annotated human genome (or transcriptome). Then, count the number of reads for each gene (or transcript), and decide on a condition to call a gene (or transcript) present in the sample (typically by enrichment between two sets of samples, in your case a threshold might be good enough). Finally, for the genes (or transcripts) present in the sample, find out what protein (or isoform) they correspond to, and if needed retrieve the sequence.
  To be clear, you will have to learn a lot more to get that done. For the first step, easier tools might include kallisto or salmon. You would probably want to use biological replicates; SRP237926 seems to have several samples, reading the paper would be necessary to determine whether they are useful.
  
original_text: 15408: <p>Forgive the basic question here, but I'm super novice at this ...</p>
  <p>I have a series of paired-end RNA fastq files (e.g. <code>SRR10720226_1.fastq.gz</code> and <code>SRR10720226_2.fastq.gz</code>).  I'm trying to figure out what software I need to use to translate those into proteins.</p>
  <p>I was trying to use <code>biopython</code> to do this using the <code>translate</code> method.  The problem is <code>biopython</code> doesn't seem to consider both files together, only one <code>fastq</code> at a time.</p>
  <p>Which tool should I use to work with the reads together?  Is there anything else I should be doing besides just translating to protein?</p>
   9497: <p>This is a much more complicated question than it might seem.</p>
  <p>First, you need to understand how RNA-Seq works, and what your data really is. Your &quot;paired-end files&quot; contain reads, which will contain fragments of transcripts.</p>
  <p>Since those are only fragments of transcripts, you don't know what frame they are in, so you don't have a single possible translation. And each read would only give you a small part of the protein.</p>
  <p>Since the data is for humans, your best course of action would be to first, align the reads to the annotated human genome (or transcriptome). Then, count the number of reads for each gene (or transcript), and decide on a condition to call a gene (or transcript) present in the sample (typically by enrichment between two sets of samples, in your case a threshold might be good enough). Finally, for the genes (or transcripts) present in the sample, find out what protein (or isoform) they correspond to, and if needed retrieve the sequence.</p>
  <p>To be clear, you will have to learn a lot more to get that done. For the first step, easier tools might include <a href="https://pachterlab.github.io/kallisto/about" rel="nofollow noreferrer">kallisto</a> or <a href="https://salmon.readthedocs.io/en/latest/salmon.html" rel="nofollow noreferrer">salmon</a>. You would probably want to use biological replicates; SRP237926 seems to have several samples, reading the paper would be necessary to determine whether they are useful.</p>
  