<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>

CC BY-SA 4.0
2020-05-27T17:49:17.580Z
Dear @Dan absolutely, yes, however you would need to explain what you are working on and what your biological objectives are.
M__
CC BY-SA 4.0
2020-05-28T12:13:05.067Z
@Michael, Thanks for the comment. I am not sure why that is specifically relevant here, but I am happy to do so.
Dan
CC BY-SA 4.0
2020-05-28T12:25:31.050Z
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.
M__
CC BY-SA 4.0
2020-05-28T12:26:41.503Z
@Michael That makes sense, thanks for the clarification!
Dan
CC BY-SA 4.0
2020-05-28T12:59:04.713Z
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`.
Kamil S Jaron
CC BY-SA 4.0
2020-06-29T12:47:56.360Z
Any further feedback @Michael?
Dan
CC BY-SA 4.0
2020-06-29T13:29:00.027Z
...  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.
M__
<fasta><identifiers><igv><nomenclature>
Is there a FASTA Sequence Description Nomenclature to Indicate a Split Sequence or Subsequence?
# 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.

Is there a standard FASTA sequence description nomenclature for subsequences to accomplish what I'm describing that is recognized by programs like IGV?
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 @Dan 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 @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.  
> **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 @KamilSJaron advice.  

---

## 0 answers

