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  • Edoardo
    Junior Member
    • Mar 2016
    • 2
    #1

    Problem using SnpEff after Transdecoder: large number of warnings

    Hi,
    I am a PhD student with very little experience in bioinformatics (or very little experience at all, I started two months ago).
    I’m having some problems getting Snpeff to work with gff coordinates obtained by Transdecoder.
    I was given by a group with which I am collaborating the assembly of a genome and a gtf file with transcript information derived from RNAseq. I used Transdecoder following the instructions, with the –single_best_orf option, and I got the cds file and a gff3.
    I used the gff3 to build a database for snpeff, because I have to evaluate the effect of some SNPs on the genome. Howevere, when I launched Snpeff eff, I received a great number of warnings:

    INFO_REALIGN_3_PRIME 1
    WARNING_TRANSCRIPT_NO_START_CODON 202855
    WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME 2
    WARNING_TRANSCRIPT_NO_STOP_CODON 17281

    Protein coding transcripts : 2426
    # Length errors : 0 ( 0,00% )
    # STOP codons in CDS errors : 0 ( 0,00% )
    # START codon errors : 686 ( 28,28% )
    # STOP codon warnings : 183 ( 7,54% )
    # UTR sequences : 2409 ( 99,30% )
    # Total Errors : 686 ( 28,28% )

    Given the low number of transcripts, this amount of warnings seems to be extremely high. Is it normal?
    Also, I checked the CDSs obtained by Transdecoder and, even if not all of them start with ATG, all of them have a start codon near the beginning of the sequence, so I really cannot explain this number of warnings.
    Do you have any suggestions?
    May the life of he/she who comes to my aid be filled with cakes and pizzas.
    Best Regards
    Edoardo
    Tags: find cds, snpeff, transdecoder
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