Hello, I need the gene description file for rice (japonica and indica both) for my RNASeq annotation work.
1. can anyone direct me to the source?
2. What is the file format for such a file?
There are several possible file formats for gene description/gene definitions. If you tell us which program you intend to use we can better tell you which format you'll need. So, for rize I have found gene definitions in GTF and GFF format here: http://plants.ensembl.org/info/website/ftp/index.html
Hello Peter,
actually I m using gfold for my data. It calculates in 2 steps- count (count reads) and diff (tells the differentially expressed genes)
I did download the japonica.gtf file from Illumina iGenomes for annotation, which is to be done in "count" using the flag -ann
For "diff" we need to use -d in the command line specifying the gene description file for it . So, I got confused.
However, I tried using the same japonica.gtf file with -d, but it didn't work, still the gene description column has no results.
Can you please help?
They specify how the file should be built but I do not see an apparent reason why this is needed and can not be extracted from the GTF file. So, you could try to build that file yourself (I think they state one column should be the gene description and the other the gene id), or you could try to use some other software to analyze differential expression (try e.g. DeSeq2)
can you give some idea how to re-format the .gtf according to the gfold manual. I need to use this software as we don't have biological replicates.
I am actually not sure how the GTF file is build but it could work something like this in a Linux terminal. Let's assume the gene id field is in column 12 and the gene description is in column 10
cat japonica.gtf | awk '{print $10"\t"$12}' > output.definition
However, I am not sure about the GTF format, where the important columns are stored etc.
Also I have to mention (but I assume you know that): not having replicates in differential expression is considered bad experimental design. While I do not know the reasons for your choice, you will probably not be able to discern technical from biological noise...
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