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  • Creating new FA by extracting particular annotation (GTF) and sequence (reference FA)

    I've got some list of differentially expressed genes.
    Then, as a next step, I want to do blast.

    Before doing blast, I want to make a new fasta file.
    Regarding the genes that are identified as differentially expressed,
    I would like to extract the position of those genes from annotation.gtf,
    and, based on this position, extract the sequence from reference.fasta.

    Then, with this new fasta file, I want to do blast.
    Would you recommend some way to do this? Is there a software which has this function other than galaxy or gffread?

    Thank you in advance.
    Last edited by syintel87; 02-06-2013, 02:57 PM.

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