gene info from XLOC

[ojham]

Hello Everyone,
I am new to genomics. I am using cuffdiff to get differentially expressed genes. and as output, I am getting the gene_id as XLOC_......, can anybody help me extracting useful gene information, gene name from XLOC ids ?

Any help is appreciated.
Thank You

[pbluescript]

Hello Everyone,
I am new to genomics. I am using cuffdiff to get differentially expressed genes. and as output, I am getting the gene_id as XLOC_......, can anybody help me extracting useful gene information, gene name from XLOC ids ?

Any help is appreciated.
Thank You

The best way is to supply a GTF file to Cufflinks/Cuffdiff before you run the program using the -G option. Is this an organism with a good annotation?

[ojham]

Hi, thank you for the response. I did use -G option while doing cufflink and yes the data is annotated data. Do I need to use -G option for cuffdiff also ?

[pbluescript]

Cuffdiff doesn't have a -G option since a GTF file is a requirement rather than an option. Does your GTF file have gene names in it? Does the Cufflinks output have the correct annotation?

[ojham]

yes my GTF file has gene names in it . how do I find if the annotation is correct or not , to which file I have to compare ?

[pbluescript]

Could you post a couple lines of your gtf file?

[ojham]

I have attached data for two gene Ids

[pbluescript]

I meant the actual gtf file you used as input for cufflinks. You need to make sure it fits the format specified in the cufflinks manual.

[ojham]

is this one you want ?

[pbluescript]

Yes, that looks like a proper gtf file, but it does not have a gene name associated with any of the entries, so there will be no gene name associated with any of the cufflinks output. You need to either find a new gtf file for your organism that has gene names or update the file to contain gene names.

[ojham]

thank you. I will find gtf file with gene name and repeat the process and will update the result.

[ojham]

I have a query, this cufflink's gtf file wil be used as reference gtf file for all the samples. and if I update the gtf file with gene names then this will work for current sample , but not for other samples. what should I do in that case ?

[ojham]

Finally !!! cuffdiff is able to generate corresponding gene IDs for XLOC IDs. I did tophat>>cuffcompare>>cufdiff.

[ojham]

pbluescript,

can you explain me how FPKM values are calculated in cuffdiff output. I have used two samples long and short and each have 3 groups as L1,L2, L3 and S1, S2, S3. I used cuffdiff on these 6 data sets assuming them as two different types

[pbluescript]

pbluescript,

can you explain me how FPKM values are calculated in cuffdiff output. I have used two samples long and short and each have 3 groups as L1,L2, L3 and S1, S2, S3. I used cuffdiff on these 6 data sets assuming them as two different types

Have you read through the manual at the Cufflinks webpage?
Specifically, this section should be useful:

http://cufflinks.cbcb.umd.edu/howitworks.html