text: user8601: I am looking at the videos at a DIY Transcriptomics course and the speaker mentions that to run Kallisto for read alignment with paired end sequencing, one would enter the following:
  
  where the sample files at the end refer to the two different end reads (forward and reverse read files). However, browsing the NCBI for paired end data, I noticed that only 1 Fastq file is provided per replicate for a paired end procedure (here's an example). So I'm a bit confused about this. 
  
  user35: The problem is that the SRA website can be a little confusing. View the same project on ENA where the organization is more human-readable: https://www.ebi.ac.uk/ena/browser/view/PRJNA574273
  
original_text: 8601: <p>I am looking at the videos at a <a href="http://diytranscriptomics.com/" rel="nofollow noreferrer">DIY Transcriptomics course</a> and the speaker mentions that to run Kallisto for read alignment with paired end sequencing, one would enter the following:</p>
  
  <p><a href="https://i.stack.imgur.com/3w2hf.png" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/3w2hf.png" alt="enter image description here"></a></p>
  
  <p>where the sample files at the end refer to the two different end reads (forward and reverse read files). However, browsing the NCBI for paired end data, I noticed that only 1 Fastq file is provided per replicate for a paired end procedure (<a href="https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA574273&amp;o=acc_s%3Aa" rel="nofollow noreferrer">here</a>'s an example). So I'm a bit confused about this. </p>
   35: <p>The problem is that the SRA website can be a little confusing. View the same project on ENA where the organization is more human-readable: <a href="https://www.ebi.ac.uk/ena/browser/view/PRJNA574273" rel="nofollow noreferrer">https://www.ebi.ac.uk/ena/browser/view/PRJNA574273</a></p>
  