<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>

CC BY-SA 4.0
2021-02-05T17:23:56.223Z
Does the file named `HCV_rna_paired.txt` exist? Is it in the directory from which you run this R script?
terdon
CC BY-SA 4.0
2021-02-06T20:47:39.247Z
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.
hko
CC BY-SA 4.0
2021-02-08T08:03:38.567Z
Definitely a file not found problem. Try: mydat<-scan("HCV_rna_paired.txt",what="",n=10) and see if it gives the same error
Fabio Marroni
<rna-seq><phylogenetics><bioconductor>
Trouble aligning next generation sequencing data to reference genomes using QuasR package in Bioconductor. Cannot import .txt
# 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  

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## 0 answers

