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  • NDUFB11
    started a topic Transcriptome Generation -Salmon

    Transcriptome Generation -Salmon

    Hello guys,

    I'm analyzing the gene expression profiling in nematode and I want to generate a FASTA file containing the sequence of all the transcripts using Salmon.

    It seems that the program can't find a fasta file although I checked and I have in the genome folder named transcripts.fa

    It might be that this file contain a sort of error?

    Here is the code

    Code:
    Patrizios-MBP:processing patrizio$ gffread -w genome/transcripts.fa -g genome/ce11.fa annotation/ce11_genes.gtf
    Warning: couldn't find fasta record for 'I'!
    Warning: getSpliced(NULL,.. ) called!
    Warning: couldn't find fasta record for 'I'!
    Warning: getSpliced(NULL,.. ) called!
    Warning: couldn't find fasta record for 'I'!
    Warning: getSpliced(NULL,.. ) called!
    Warning: couldn't find fasta record for 'I'!


    Thank you

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