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Identifying genes from contigs (obtained from transcriptome of a fungi)

Hello,

I have a query regarding identifying genes from the transcriptome data of a fungi. I got a fasta file containing contigs from my lab member and I need to identify the genes of my interests from those contigs.

What I have done so far is that I have performed blastx of the all the contigs againts nr database. I got the match for the contigs but I am confused with the query frames, as sometimes they are negative? More over when I take a positive frame as per the hit, I get some translated protein sequence which matched to the hit but the match is never complete because I get stop codons in between. So I am confused whether I am doing it the right way or not?

Any help would be appreciated.

Regards BHARAT

gene contigs transcriptome
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updated by mikhail.shugay mikhail.shugay • written by bharat.85.monu • bharat.85.monu

1 answer

Check out Transdecoder and other downstream analysis options from Trinity pipeline.

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written by mikhail.shugay mikhail.shugay

Thanks Mikhail for the answer. Could you please let me know whether its possible to assemble the entire genome only from the contigs. Actually, I am new to this area and I hope you will answer accordingly. What I have with me is only a file containing contigs and I don't know whether they are paired-end or not ? I don't even know whether paired end reads are required for further assembly or not ??

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written by bharat.85.monu • bharat.85.monu

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