Body: <p>I'm trying to check the quality of my paired end read sequencing data. I am following this pipeline (<a href="https://f1000research.com/articles/4-1062#ref-21" rel="nofollow noreferrer">https://f1000research.com/articles/4-1062#ref-21</a>) which uses QuasR in the first step.</p>
  <p>My list of paired files is stored in <code>sampleFile</code>. Currently this file cannot be read into the function. Not sure why. I'm using R studio on a windows operating system.</p>
  <p>Also open to using other alignment or QC pathways if I can align to multiple different genomes.</p>
  <pre><code>auxFile &lt;- &quot;Ref_Genomes/auxiliaries.txt&quot;
  sampleFile &lt;- &quot;./HCV_rna_paired.txt&quot;
  genomeName &lt;- &quot;BSgenome.Hsapiens.UCSC.hg38&quot;
  td &lt;- tempdir()
      
  proj1&lt;- qAlign(sampleFile, genome=genomeName, auxiliaryFile=auxFile)
  </code></pre>
  <blockquote>
  <p>Error: cannot open ./HCV_rna_paired.txt</p>
  </blockquote>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2021-02-05T17:23:56.223Z
Comments.Text: Does the file named `HCV_rna_paired.txt` exist? Is it in the directory from which you run this R script?
Comments.UserDisplayName: terdon
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2021-02-06T20:47:39.247Z
Comments.Text: Yes the file exists in the same directory in which I was running commands. 
  As for the error message, would I receive the same message if it was a path error? I will try this next.
Comments.UserDisplayName: hko
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2021-02-08T08:03:38.567Z
Comments.Text: Definitely a file not found problem. Try: mydat<-scan("HCV_rna_paired.txt",what="",n=10) and see if it gives the same error
Comments.UserDisplayName: Fabio Marroni
Tags: <rna-seq><phylogenetics><bioconductor>
Title: Trouble aligning next generation sequencing data to reference genomes using QuasR package in Bioconductor. Cannot import .txt
ThreadText: # Trouble aligning next generation sequencing data to reference genomes using QuasR package in Bioconductor. Cannot import .txt
  
  (Asked by: username_0 on 2021-02-05)
  
  I'm trying to check the quality of my paired end read sequencing data. I am following this pipeline (<https://f1000research.com/articles/4-1062#ref-21>) which uses QuasR in the first step.
  
  My list of paired files is stored in `sampleFile`. Currently this file cannot be read into the function. Not sure why. I'm using R studio on a windows operating system.
  
  Also open to using other alignment or QC pathways if I can align to multiple different genomes.
  
  ```
  auxFile <- "Ref_Genomes/auxiliaries.txt"
  sampleFile <- "./HCV_rna_paired.txt"
  genomeName <- "BSgenome.Hsapiens.UCSC.hg38"
  td <- tempdir()
      
  proj1<- qAlign(sampleFile, genome=genomeName, auxiliaryFile=auxFile)
  
  ```
  
  > Error: cannot open ./HCV\_rna\_paired.txt
  
  **Tags:** rna-seq, phylogenetics, bioconductor
  
  > **Comments:**
  > **username_1**: Does the file named `HCV_rna_paired.txt` exist? Is it in the directory from which you run this R script?  
  > **username_0**: Yes the file exists in the same directory in which I was running commands.  As for the error message, would I receive the same message if it was a path error? I will try this next.  
  > **username_2**: Definitely a file not found problem. Try: mydat<-scan("HCV_rna_paired.txt",what="",n=10) and see if it gives the same error  
  
  ---
  
  ## 0 answers
  
  