A Python script to identify noncoding Natural Antisense Transcripts (NATs) from AceView transcriptomic database.
Usage:
- Download AceView GTF file from:
human: ftp://ftp.ncbi.nih.gov/repository/acedb/ncbi_37_Aug10.human.genes/AceView.ncbi_37.genes_gff.gff.gz
mouse: ftp://ftp.ncbi.nih.gov/repository/acedb/ncbi_37_Sep07.mouse.genes/AceView.mm_37.genes_gff.tar.gz
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Untar the archive into the directory with the Python script.
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Run the script and type in "filter" when asked for mode. Choose your GTF file. The script will filter and sort the GTF file and will save it with "_filtered" suffix.
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Prepare the list of genes of interest to look for NATs. The file should be in text format containing official gene symbols, one per line.
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Save the input file in the same folder with the script and the GTF file.
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Run the script again, this time type type in "find" when asked for mode.
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Specify the reference GTF file (filtered and sorted) and the input file.
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After search is done type in the output file name.
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The output will be saved in the file.