vg build graph for transcripts of a gene

Question

[Logan YL Chen]

How could I create a graph reference for a gene with different transcripts sequences?

I have created a fasta file that contained several transcripts sequences of a certain gene, as below example:

>transcript1
ATCGATCGATCG
>transcript2
ATCGATCGAACG
>transcript3
ATCGATCGAGGG

and ran the vg construct to build the graph for this fasta(without any variants vcf).

In my mind, I should get a graph like

          /GG\
 ATCGATCGA-TCG
          \A/

but I've got three separate graphs. I don't know is that normal or I used the wrong function. I may need someone to give me some advise. Sorry, if this was quite an easy question.

[Ram]

Please use the formatting bar (especially the code option) to present your post better. You can use backticks for inline code (`text` becomes text), or select a chunk of text and use the highlighted button to format it as a code block. I've done it for you this time.

[Logan YL Chen]

Thank you very much.

Answer 1

[LilithElina]

You didn't add the vg construct command you used, so I can only guess: did you use the -M option to specify that you have multiple sequences as input? If that doesn't work, you could try vg msga instead.

[Logan YL Chen]

I only used vg construct xxx.fasta > xxx.vg. I will try what you suggest. Thanks.