Body: <p>I have a nucleotide sequence where I am interested in aligning reads distinctly to one or another portion of the sequence. However, I would like to use a visualization tool such as IGV to view these alignments in the context of the parent sequence. For example, I would like to split something along the lines of:</p>
  
  <pre><code>&gt;seq1 parent_sequence
  ACTGACTGACTGACTGACTGGTCAGTCAGTCAGTCAGTCAACACACACACACACACACAC
  </code></pre>
  
  <p>Into:</p>
  
  <pre><code>&gt;seq1_1:20 parent_sequence subsequence_1_to_20
  ACTGACTGACTGACTGACTG
  &gt;seq1_21:40 parent_sequence subsequence_21_to_40
  GTCAGTCAGTCAGTCAGTCA
  &gt;seq1_41:60 parent_sequence subsequence_41_to_60
  ACACACACACACACACACAC
  </code></pre>
  
  <p>Then perform alignments using the split subsequences as a reference for alignment of reads, but visualize these read alignments on the parent sequence.</p>
  
  <p>While I'm sure it would be possible to write a script to manipulate all the alignments to all of the "split" subsequences back into the context of their original parent sequence, I am trying to avoid this if possible.</p>
  
  <ol>
  <li>Is there a standard FASTA sequence description nomenclature for subsequences to accomplish what I'm describing that is recognized by programs like IGV?</li>
  <li>If there is not, I will likely still be splitting these sequences as described. Is there a suggested standard/common method for annotating/identifying these split sequence identifiers that maximizes readability?</li>
  </ol>
  
  <p><strong>Edit:</strong></p>
  
  <p>The biological context for this question is analysis of RNA-Seq data collected after pulldown of a specific RNA-binding protein and digestion of overhanging read ends. The data should be enriched for a specific subsequence of interest, but will also contain the "parent" transcript. Alignments to both portions are of interest to me, but in different ways, and the alignments to the subsequence and the remainder of the parent sequence should be considered distinct. In terms of visualization it is helpful to view the alignments to all pieces in context of the "parent" transcript. </p>
  
  <p>I realize that splitting the parent sequence into two subsequences for alignment will result in loss of reads straddling the two portions, but that is acceptable given the necessity of having the two sections be distinct for alignment purposes.</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-05-27T17:49:17.580Z
Comments.Text: Dear @Dan absolutely, yes, however you would need to explain what you are working on and what your biological objectives are.
Comments.UserDisplayName: M__
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-05-28T12:13:05.067Z
Comments.Text: @Michael, Thanks for the comment. I am not sure why that is specifically relevant here, but I am happy to do so.
Comments.UserDisplayName: Dan
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-05-28T12:25:31.050Z
Comments.Text: Dear @Dan, thanks biological aims and organism/field are frequently requested particularly where there is very little technical information, particularly code. It is quite common to encounter situations where the OP says, "thats not what I meant" following an answer.
Comments.UserDisplayName: M__
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-05-28T12:26:41.503Z
Comments.Text: @Michael That makes sense, thanks for the clarification!
Comments.UserDisplayName: Dan
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-05-28T12:59:04.713Z
Comments.Text: IMHO there is a widely accepted standard for split reference fasta headers, there could be something IGV specific though. When I do subsequences, I do `>REF_from_to`.
Comments.UserDisplayName: Kamil S Jaron
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-06-29T12:47:56.360Z
Comments.Text: Any further feedback @Michael?
Comments.UserDisplayName: Dan
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-06-29T13:29:00.027Z
Comments.Text: ...  in my area mixed infections are a big issue, hence my question. So if you use Illumina short-reads its complicated. If you are dealing with mRNA  .... follow @KamilSJaron advice.
Comments.UserDisplayName: M__
Tags: <fasta><identifiers><igv><nomenclature>
Title: Is there a FASTA Sequence Description Nomenclature to Indicate a Split Sequence or Subsequence?
ThreadText: # Is there a FASTA Sequence Description Nomenclature to Indicate a Split Sequence or Subsequence?
  
  (Asked by: username_0 on 2020-05-27)
  
  I have a nucleotide sequence where I am interested in aligning reads distinctly to one or another portion of the sequence. However, I would like to use a visualization tool such as IGV to view these alignments in the context of the parent sequence. For example, I would like to split something along the lines of:
  
  ```
  >seq1 parent_sequence
  ACTGACTGACTGACTGACTGGTCAGTCAGTCAGTCAGTCAACACACACACACACACACAC
  
  ```
  
  Into:
  
  ```
  >seq1_1:20 parent_sequence subsequence_1_to_20
  ACTGACTGACTGACTGACTG
  >seq1_21:40 parent_sequence subsequence_21_to_40
  GTCAGTCAGTCAGTCAGTCA
  >seq1_41:60 parent_sequence subsequence_41_to_60
  ACACACACACACACACACAC
  
  ```
  
  Then perform alignments using the split subsequences as a reference for alignment of reads, but visualize these read alignments on the parent sequence.
  
  While I'm sure it would be possible to write a script to manipulate all the alignments to all of the "split" subsequences back into the context of their original parent sequence, I am trying to avoid this if possible.
  
  1. Is there a standard FASTA sequence description nomenclature for subsequences to accomplish what I'm describing that is recognized by programs like IGV?
  2. If there is not, I will likely still be splitting these sequences as described. Is there a suggested standard/common method for annotating/identifying these split sequence identifiers that maximizes readability?
  
  **Edit:**
  
  The biological context for this question is analysis of RNA-Seq data collected after pulldown of a specific RNA-binding protein and digestion of overhanging read ends. The data should be enriched for a specific subsequence of interest, but will also contain the "parent" transcript. Alignments to both portions are of interest to me, but in different ways, and the alignments to the subsequence and the remainder of the parent sequence should be considered distinct. In terms of visualization it is helpful to view the alignments to all pieces in context of the "parent" transcript.
  
  I realize that splitting the parent sequence into two subsequences for alignment will result in loss of reads straddling the two portions, but that is acceptable given the necessity of having the two sections be distinct for alignment purposes.
  
  **Tags:** fasta, identifiers, igv, nomenclature
  
  > **Comments:**
  > **username_1**: Dear @username_0 absolutely, yes, however you would need to explain what you are working on and what your biological objectives are.  
  > **username_0**: @Michael, Thanks for the comment. I am not sure why that is specifically relevant here, but I am happy to do so.  
  > **username_1**: Dear @username_0, thanks biological aims and organism/field are frequently requested particularly where there is very little technical information, particularly code. It is quite common to encounter situations where the OP says, "thats not what I meant" following an answer.  
  > **username_0**: @Michael That makes sense, thanks for the clarification!  
  > **username_2**: IMHO there is a widely accepted standard for split reference fasta headers, there could be something IGV specific though. When I do subsequences, I do `>REF_from_to`.  
  > **username_0**: Any further feedback @Michael?  
  > **username_1**: ...  in my area mixed infections are a big issue, hence my question. So if you use Illumina short-reads its complicated. If you are dealing with mRNA  .... follow @username_2 advice.  
  
  ---
  
  ## 0 answers
  
  