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  • xuxiaochen
    Junior Member
    • Dec 2016
    • 1
    #1

    Use perl to generate FASTA formatted file

    I'm trying to generate a FASTA file listing all the differential expression gene. I have output from cuffdiff: gene_exp.diff
    And I also have a reference genome. I was trying to use perl/extractGene.pl, but I cannot get output file...

    The job file:

    perl perl/extractGene.pl -d cuffdiff_JDMCA_merge/gene_exp.diff -g HC/ref_genome.fa

    But I don't have any output. Furthermore, both the error file and o file is 0, for example: the size of both perl.o1600164 and perl.e1600164 is 0.

    I'm not sure whether I expressed this problem clearly...
    Tags: None
    • fahmida
      Member
      • Aug 2010
      • 54
      #2
      You may have to do some filtering/pre-processing etc. if you are using this script:
      A script for Cuffdiff: extract differential expression gene sequences from genome.fa - SEQanswers
      http://seqanswers.com/forums/showthread.php?t=20508
      Discussion of next-gen sequencing related bioinformatics: resources, algorithms, open source efforts, etc

      Details are there.

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