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


>seq1_1:20 parent_sequence subsequence_1_to_20
>seq1_21:40 parent_sequence subsequence_21_to_40
>seq1_41:60 parent_sequence subsequence_41_to_60

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?


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.

  • $\begingroup$ Dear @Dan absolutely, yes, however you would need to explain what you are working on and what your biological objectives are. $\endgroup$
    – M__
    May 27, 2020 at 17:49
  • $\begingroup$ @Michael, Thanks for the comment. I am not sure why that is specifically relevant here, but I am happy to do so. $\endgroup$
    – Dan
    May 28, 2020 at 12:13
  • $\begingroup$ 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. $\endgroup$
    – M__
    May 28, 2020 at 12:25
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    $\begingroup$ 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. $\endgroup$ May 28, 2020 at 12:59
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    $\begingroup$ ... 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. $\endgroup$
    – M__
    Jun 29, 2020 at 13:29


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