Human genome annotation
hello, I want to create gene annotation (gff) file with human genome (gtf) file using HTSeq with DESeq package. The scripts "python /path/to/library/DEXSeq/python_scripts/dexseq_prepare_annotation.py Drosophila_melanogaster.BDGP5.72.gtf Dmel.BDGP5.25.62.DEXSeq.chr.gff" giving by DESeq package guide within my own data give me this error "SyntaxError: illegal target for annotation"0
Help please even if there are any way to generate annotation.
Best regard.
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justinkablan225 •
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Do you really need to annotate the human genome? It is probably the best annotated eukaryotic genome. And why are you using a Drosophila melanogaster (Dmel.BDGP5.25.62.DEXSeq.chr.gff) annotation?
dexseq_prepare_annotation.pyscript is not to annotate anything. It just "flattens" the GTF file so that flattened GTF its compatible with DEXseq tool. I am not sure why are you creating human gene annotation usingdexseq_prepare_annotation.pywith Drosophila GTF.This is what I done in python command line shell following the guide below :
"python C:/Users/Justin KA/Documents/R/win-library/3.5/DEXSeq/python_scripts/dexseq_prepare_annotation.py Homo_sapiens.GRCh38.95.gtf chr_H_G_38_95.gff "
Guide :
Make sure that your current working directory contains the GTF file and call the script (from the command line shell, not from within R) with python /path/to/library/DEXSeq/python_scripts/dexseq_prepare_annotation.py Drosophila_melanogaster.BDGP5.72.gtf Dmel.BDGP5.25.62.DEXSeq.chr.gff In this command, which should be entered as a single line, replace /path/to.../python_ scripts with the correct path to the Python scripts, which you have found with the call to system.file shown above. Drosophila_melanogaster.BDGP5.72.gtf is the Ensembl GTF file (here the one for fruit fly, already de-compressed) and Dmel.BDGP5.25.62.DEXSeq.chr.gff is the name of the output file.
This is what I done in python command line shell following the guide below :
"python C:/Users/Justin KA/Documents/R/win-library/3.5/DEXSeq/python_scripts/dexseq_prepare_annotation.py Homo_sapiens.GRCh38.95.gtf chr_H_G_38_95.gff "
Guide :
Make sure that your current working directory contains the GTF file and call the script (from the command line shell, not from within R) with python /path/to/library/DEXSeq/python_scripts/dexseq_prepare_annotation.py Drosophila_melanogaster.BDGP5.72.gtf Dmel.BDGP5.25.62.DEXSeq.chr.gff In this command, which should be entered as a single line, replace /path/to.../python_ scripts with the correct path to the Python scripts, which you have found with the call to system.file shown above. Drosophila_melanogaster.BDGP5.72.gtf is the Ensembl GTF file (here the one for fruit fly, already de-compressed) and Dmel.BDGP5.25.62.DEXSeq.chr.gff is the name of the output file.