Hi all,
We sequenced the genome and the transcriptome of a non-model invertebrate
We made denovo assembly for both.
Now, we have 1000's of scaffolds + 1000's of transcripts.
We want to use this information for getting the full picture of some gene of interest.
For example, we have Transcript X which isnt full length, we want to find the rest of it in the genome.
What we thoght about is to first find which are the exons/introns in the genome, and then to search for the rest of the desire transcript.
I used ORF finder, but the output is too complicated when the input is 50K bp.
I also used AUGUSTUS, but my organism inst in there list so i used C-elegans, and the output didnt have any match using blast.
Any ideas will be meaningful..
Thanks,
Pap
We sequenced the genome and the transcriptome of a non-model invertebrate
We made denovo assembly for both.
Now, we have 1000's of scaffolds + 1000's of transcripts.
We want to use this information for getting the full picture of some gene of interest.
For example, we have Transcript X which isnt full length, we want to find the rest of it in the genome.
What we thoght about is to first find which are the exons/introns in the genome, and then to search for the rest of the desire transcript.
I used ORF finder, but the output is too complicated when the input is 50K bp.
I also used AUGUSTUS, but my organism inst in there list so i used C-elegans, and the output didnt have any match using blast.
Any ideas will be meaningful..
Thanks,
Pap
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