Use perl to generate FASTA formatted file

[xuxiaochen]

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...

[fahmida]

You may have to do some filtering/pre-processing etc. if you are using this script:

http://seqanswers.com/forums/showthread.php?t=20508

Details are there.