Answers.Body: <blockquote>
  <p>With the data attached above, would my N50 and N90 length in BASE PAIRS so excluding the kb, be 7464 and 14314, respectively?</p>
  </blockquote>
  <p>Looks like this is inverse so your N50 is 1032bp and your N90 is 106bp. N90 cannot be longer than N50 by definition. You L50 and L90 are 7464 and 14314</p>
  <blockquote>
  <p>Would the number of contigs produced by this assembly be 7, since there are 7 different contigs produced or would it be 25,534?</p>
  </blockquote>
  <p>25534</p>
  <p>Now for the real answer. <strong>Do not calculate or report N50 on transcript assemblies. It is more than useless.</strong> Transcriptomes are - by nature - dynamic in length. Longer is not better in this regard. Are your short transcripts lower quality assemblies, probably not, but N50 treats them as such. Please read the <a href="https://github.com/trinityrnaseq/trinityrnaseq/wiki/Transcriptome-Assembly-Quality-Assessment" rel="nofollow noreferrer">Trinity wiki</a> for other, better ways to QC your transcript assembly.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-11-12T23:22:53.760Z
Answers.Text: Hi @BastianSchiffthaler, thank you for your help! Ok so basically, one is the count and one is the length. Therefore, would my N50 length be 1032bp or is that my count? Then would 7464 be my length?
Answers.UserDisplayName: AlphaQueUp
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-11-12T23:50:18.333Z
Answers.Text: Also, say if my N50 length is base pairs was 1032 and I wanted to find out "how many contigs are as long or longer than then the length of 1032; would this simply just be 25,534 - 1032 = 24,502? Thanks! @Bastian Schiffthaler
Answers.UserDisplayName: AlphaQueUp
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-11-13T00:03:31.750Z
Answers.Text: Let's say you order your contigs from longest to shortest. After that, you calculate the sum of all contig lengths, i.e. the total length of your assembly. Now you go from the longest contig to the shortest until the cumulative sum reaches >=50% of the total length. The length of the contig at that position is the N50, the number of contigs you had to include to reach 50% is the L50. N50 = length = 1032bp. L50 = count = 7464. 25534 − 7464 = 18070 contigs are _shorter_ than your N50.
Answers.UserDisplayName: Bastian Schiffthaler
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-11-13T03:02:34.437Z
Answers.Text: So then that would simply just mean that 7464 contigs are as long or longer than my N50 @BastianSchiffthaler and 14314 for N90? I apologize for the repetitive questions. I am just starting to learn bioinformatics, so this is all a new language to me. I appreciate all your help!
Answers.UserDisplayName: AlphaQueUp
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-11-13T15:41:55.140Z
Answers.Text: Yes. That's correct
Answers.UserDisplayName: Bastian Schiffthaler
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-11-14T03:07:17.473Z
Answers.Text: Thank you very much! @BastianSchiffthaler
Answers.UserDisplayName: AlphaQueUp
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-11-14T22:01:06.373Z
Answers.Text: Hi @BastianSchiffthaler, I was wondering if I could get your advice for one of my commands? Thanks!
Answers.UserDisplayName: AlphaQueUp
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-11-14T22:01:11.187Z
Answers.Text: Hi @Bastian Schiffthaler, I was wondering if I could get your advice for one of my commands? Thanks!
Answers.UserDisplayName: AlphaQueUp
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-11-15T00:59:40.417Z
Answers.Text: Please open a separate question.
Answers.UserDisplayName: Bastian Schiffthaler
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-11-12T20:09:30.733Z
Answers.LastActivityDate: 2020-11-12T20:09:30.733Z
Answers.UserDisplayName: Bastian Schiffthaler
Body: <p>I am having trouble with some underlying questions about my project.</p>
  <p>I have ran a Trinity tool to create a trinity.fasta file.</p>
  <p>To determine some underlying questions, I used the utility asm_stats to gather some basic statistics.</p>
  <p>I am just having some issues of calculating data.</p>
  <p>DATA:</p>
  <p>Main genome scaffold N/L50: 7464/1.032 KB<br />
  Main genome contig N/L50: 7464/1.032 KB<br />
  Main genome scaffold N/L90: 14314/106<br />
  Main genome contig N/L90: 14314/106</p>
  <p>Number of contigs (scaffold length):</p>
  <p>25,534 (ALL)<br />
  25,534 (100)<br />
  21,609 (250)<br />
  10,818 (500)<br />
  907 (1 KB)<br />
  38 (2.5KB)<br />
  5 (5 KB)<br />
  2 (10KB)</p>
  <p>With the data attached above, would my N50 and N90 length in <strong>BASE PAIRS</strong> so excluding the kb, be 7464 and 14314, respectively?</p>
  <p><em>Would the number of contigs produced by this assembly</em> be 7, since there are 7 different contigs produced or would it be 25,534?</p>
  <p>Thanks!</p>
  
Tags: <rna-seq><fasta><fastq><file-formats>
Title: How to find the number of contigs produced? N50 length in base pairs? N90 length in base pairs?
ThreadText: # How to find the number of contigs produced? N50 length in base pairs? N90 length in base pairs?
  
  (Asked by: username_0 on 2020-11-12)
  
  I am having trouble with some underlying questions about my project.
  
  I have ran a Trinity tool to create a trinity.fasta file.
  
  To determine some underlying questions, I used the utility asm\_stats to gather some basic statistics.
  
  I am just having some issues of calculating data.
  
  DATA:
  
  Main genome scaffold N/L50: 7464/1.032 KB  
  Main genome contig N/L50: 7464/1.032 KB  
  Main genome scaffold N/L90: 14314/106  
  Main genome contig N/L90: 14314/106
  
  Number of contigs (scaffold length):
  
  25,534 (ALL)  
  25,534 (100)  
  21,609 (250)  
  10,818 (500)  
  907 (1 KB)  
  38 (2.5KB)  
  5 (5 KB)  
  2 (10KB)
  
  With the data attached above, would my N50 and N90 length in **BASE PAIRS** so excluding the kb, be 7464 and 14314, respectively?
  
  *Would the number of contigs produced by this assembly* be 7, since there are 7 different contigs produced or would it be 25,534?
  
  Thanks!
  
  **Tags:** rna-seq, fasta, fastq, file-formats
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2020-11-12. Score: 1 | Accepted answer
  
  > With the data attached above, would my N50 and N90 length in BASE PAIRS so excluding the kb, be 7464 and 14314, respectively?
  
  Looks like this is inverse so your N50 is 1032bp and your N90 is 106bp. N90 cannot be longer than N50 by definition. You L50 and L90 are 7464 and 14314
  
  > Would the number of contigs produced by this assembly be 7, since there are 7 different contigs produced or would it be 25,534?
  
  25534
  
  Now for the real answer. **Do not calculate or report N50 on transcript assemblies. It is more than useless.** Transcriptomes are - by nature - dynamic in length. Longer is not better in this regard. Are your short transcripts lower quality assemblies, probably not, but N50 treats them as such. Please read the [Trinity wiki](https://github.com/trinityrnaseq/trinityrnaseq/wiki/Transcriptome-Assembly-Quality-Assessment) for other, better ways to QC your transcript assembly.
  
  > **Comments:**
  > **username_0**: Hi @username_1, thank you for your help! Ok so basically, one is the count and one is the length. Therefore, would my N50 length be 1032bp or is that my count? Then would 7464 be my length?  
  > **username_0**: Also, say if my N50 length is base pairs was 1032 and I wanted to find out "how many contigs are as long or longer than then the length of 1032; would this simply just be 25,534 - 1032 = 24,502? Thanks! @username_1  
  > **username_1**: Let's say you order your contigs from longest to shortest. After that, you calculate the sum of all contig lengths, i.e. the total length of your assembly. Now you go from the longest contig to the shortest until the cumulative sum reaches >=50% of the total length. The length of the contig at that position is the N50, the number of contigs you had to include to reach 50% is the L50. N50 = length = 1032bp. L50 = count = 7464. 25534 − 7464 = 18070 contigs are _shorter_ than your N50.  
  > **username_0**: So then that would simply just mean that 7464 contigs are as long or longer than my N50 @username_1 and 14314 for N90? I apologize for the repetitive questions. I am just starting to learn bioinformatics, so this is all a new language to me. I appreciate all your help!  
  > **username_1**: Yes. That's correct  
  > **username_0**: Thank you very much! @username_1  
  > **username_0**: Hi @username_1, I was wondering if I could get your advice for one of my commands? Thanks!  
  > **username_0**: Hi @username_1, I was wondering if I could get your advice for one of my commands? Thanks!  
  > **username_1**: Please open a separate question.  
  
  ---
  
  