Body: <p>I am currently in the process of comparing two distinct sets of genes that have been sequenced under two different conditions.</p>
  <p>My objective is to ascertain whether the expression of specific genes in my samples has been altered as a result of the conditions applied.</p>
  <p>For the alignment process, I am utilizing the the k-mer alignment (KMA) tool (<a href="https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-018-2336-6" rel="nofollow noreferrer">https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-018-2336-6</a>), which provides me with a results table for each condition.</p>
  <p>I am seeking guidance on which columns should be primarily considered in my calculations. Should I focus predominantly on the 'Score' (it is so-called <em>ConClave score (accumulated alignment score), from all reads that were accepted to match this template.</em> ) and 'Depth' columns?</p>
  <p>Or, should I instead concentrate on <em>readCount: Number of reads mapped to the template</em>?</p>
  <p>Would Log2 normalization work here?</p>
  <p><a href="https://i.sstatic.net/UmtuqWlE.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/UmtuqWlE.png" alt="enter image description here" /></a></p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-06-19T22:31:46.937Z
Comments.Text: Please provide links to the specific kmer alignment tool that you're using. LAST,  minimap2, and kraken2 could be interpreted as kmer alignment tools, but it's unlikely that you're using any of those programs.
Comments.UserDisplayName: gringer
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-06-19T22:32:39.673Z
Comments.Text: Given that you have results tables, please show a small subset of them as examples (e.g. first 10 rows); this helps understand the question you're asking.
Comments.UserDisplayName: gringer
Tags: <phylogenetics><k-mer>
Title: Guidance Required on Prioritizing Columns for Gene Expression Analysis Using KMA Tool
ThreadText: # Guidance Required on Prioritizing Columns for Gene Expression Analysis Using KMA Tool
  
  (Asked by: username_0 on 2024-06-19)
  
  I am currently in the process of comparing two distinct sets of genes that have been sequenced under two different conditions.
  
  My objective is to ascertain whether the expression of specific genes in my samples has been altered as a result of the conditions applied.
  
  For the alignment process, I am utilizing the the k-mer alignment (KMA) tool (<https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-018-2336-6>), which provides me with a results table for each condition.
  
  I am seeking guidance on which columns should be primarily considered in my calculations. Should I focus predominantly on the 'Score' (it is so-called *ConClave score (accumulated alignment score), from all reads that were accepted to match this template.* ) and 'Depth' columns?
  
  Or, should I instead concentrate on *readCount: Number of reads mapped to the template*?
  
  Would Log2 normalization work here?
  
  [![enter image description here](https://i.sstatic.net/UmtuqWlE.png)](https://i.sstatic.net/UmtuqWlE.png)
  
  **Tags:** phylogenetics, k-mer
  
  > **Comments:**
  > **username_1**: Please provide links to the specific kmer alignment tool that you're using. LAST,  minimap2, and kraken2 could be interpreted as kmer alignment tools, but it's unlikely that you're using any of those programs.  
  > **username_1**: Given that you have results tables, please show a small subset of them as examples (e.g. first 10 rows); this helps understand the question you're asking.  
  
  ---
  
  ## 0 answers
  
  