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Old 08-26-2013, 01:53 PM   #1
Location: NC

Join Date: Sep 2012
Posts: 24
Default Arabidopsis gtf for Cummerbund


The Arabidopsis gtf files (NCBI and Ensembl) have some problems (downloaded from iGenome; the NCBI version doesn't give the At numbers for all genes, in the Ensemble version, a gene name "B5 #5" doesn't allow Cummerbund to run because of the # sign, ie., all entries after running "cuff" are zeo. That can be fixed by creating a new gene.gtf file (e.g, genes_new.gtf) and running the following awk command:

awk '{ gsub(/#/, "No"); print }' genes_new.gtf

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