Human genome annotation
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2.1 years ago

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.

RNA-Seq HTSeq • 641 views
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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?

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dexseq_prepare_annotation.py script 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 using dexseq_prepare_annotation.py with Drosophila GTF.

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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.

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2.1 years ago
Buffo ★ 1.8k

You can use stringtie to annotate new mRNAs from RNAseq, but in agreement to h.mon you are trying to use drosophila to anotate human? that may be the cause of

illegal target for annotation

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