I only used vg construct xxx.fasta > xxx.vg. I will try what you suggest. Thanks.
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vg build graph for transcripts of a gene
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.
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1 answer
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.
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