Answers.Body: <p>Unless this is RNA-seq prepared with a directional library, or something else that you're sure is directional, it is irrelevant.</p>
  <p>DNA is complementary, so a DNA molecule can be turned into a sequence-able fragment with either strand given any pair of Illumina adapters and indices.</p>
  <p>As far as Illumina lingo goes, R1 is the first read that is read off the sequencer, or what people call the &quot;forward read&quot;. R2 is the second pass of the same clusters, and some people call it the &quot;reverse read&quot;. I recommend just calling them R1 and R2 reads to avoid confusion. Sequencing by synthesis produces the cleanest reads in the first pass, so R1 reads usually have better Q values. You can check this easily by comparing the quality scores with <a href="https://www.bioinformatics.babraham.ac.uk/projects/fastqc/" rel="nofollow noreferrer">fastqc</a>.</p>
  <p>You can learn more about Illumina sequencing chemistry <a href="http://nextgen.mgh.harvard.edu/IlluminaChemistry.html" rel="nofollow noreferrer">here</a>, or check out some other answers on the bioinformatics SE or biostars.</p>
  
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Answers.UserDisplayName: conchoecia
Answers.Body: <p>I think @conchoecia answer is correct but maybe not clear enough for someone making himself that question for the first time (like was my case recently).</p>
  <p>I think the simple way to explain this is that in F_NL_READ1.fq you have random reads, in mixed directions, and in F_NL_READ2.fq you have the paired read in the opposed direction for every read in F_NL_READ1.fq, but not necessarily and almost certainly, not every read in every file will go in the same sense (forward or reverse).</p>
  <p>At least for paired-end reads from Illumina.</p>
  
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Answers.Text: Since we have no idea what kind of reads the OP has, what you wrote might very well be completely wrong.
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Answers.UserDisplayName: juanjo75es
Answers.Body: <p>If this is RNASeq, then the question might have an answer (or it might be nonsense), but you have to know what kind of library prep was used.</p>
  <p>Or just align and inspect the results to figure it out.</p>
  
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Body: <p><a href="https://i.sstatic.net/8ncih.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/8ncih.png" alt="enter image description here" /></a></p>
  <p>As you can see in the picture I have two files from the paired end reads. I would assume READ1 would be forward reads and READ2 would be reverse reads, but my lab colleague told me that that might not be the case. How do I confirm?</p>
  
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Comments.Text: Hi @fullmooninu - any idea what type of data these reads are? It will help us give you an accurate answer.
Comments.UserDisplayName: conchoecia
Tags: <fasta>
Title: I have two fasta files READ1 and READ 2. How to identify which one is the reverse and the forward?
ThreadText: # I have two fasta files READ1 and READ 2. How to identify which one is the reverse and the forward?
  
  (Asked by: username_0 on 2021-10-31)
  
  [![enter image description here](https://i.sstatic.net/8ncih.png)](https://i.sstatic.net/8ncih.png)
  
  As you can see in the picture I have two files from the paired end reads. I would assume READ1 would be forward reads and READ2 would be reverse reads, but my lab colleague told me that that might not be the case. How do I confirm?
  
  **Tags:** fasta
  
  > **Comments:**
  > **username_1**: Hi @fullmooninu - any idea what type of data these reads are? It will help us give you an accurate answer.  
  
  ---
  
  ## 3 answers
  
  ### Answer by username_1 on 2021-11-01. Score: 3
  
  Unless this is RNA-seq prepared with a directional library, or something else that you're sure is directional, it is irrelevant.
  
  DNA is complementary, so a DNA molecule can be turned into a sequence-able fragment with either strand given any pair of Illumina adapters and indices.
  
  As far as Illumina lingo goes, R1 is the first read that is read off the sequencer, or what people call the "forward read". R2 is the second pass of the same clusters, and some people call it the "reverse read". I recommend just calling them R1 and R2 reads to avoid confusion. Sequencing by synthesis produces the cleanest reads in the first pass, so R1 reads usually have better Q values. You can check this easily by comparing the quality scores with [fastqc](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
  
  You can learn more about Illumina sequencing chemistry [here](http://nextgen.mgh.harvard.edu/IlluminaChemistry.html), or check out some other answers on the bioinformatics SE or biostars.
  
  
  ---
  
  ### Answer by username_2 on 2021-11-01. Score: 0
  
  I think @username_1 answer is correct but maybe not clear enough for someone making himself that question for the first time (like was my case recently).
  
  I think the simple way to explain this is that in F\_NL\_READ1.fq you have random reads, in mixed directions, and in F\_NL\_READ2.fq you have the paired read in the opposed direction for every read in F\_NL\_READ1.fq, but not necessarily and almost certainly, not every read in every file will go in the same sense (forward or reverse).
  
  At least for paired-end reads from Illumina.
  
  > **Comments:**
  > **username_3**: Since we have no idea what kind of reads the OP has, what you wrote might very well be completely wrong.  
  
  ---
  
  ### Answer by username_3 on 2021-11-01. Score: -1
  
  If this is RNASeq, then the question might have an answer (or it might be nonsense), but you have to know what kind of library prep was used.
  
  Or just align and inspect the results to figure it out.
  
  
  ---
  
  