Question: How to change stringtie gene_id names with ref_gene_id when performing featureCount
0
gravatar for IRAIA.MAIALEN
9 months ago by
IRAIA.MAIALEN0 wrote:

Hi everybody!

I would like to know if there is a way to change stringtie "geneid" with "refgene_id" when performing featureCount to construct the count table for edgeR.

The thing is that I have use stringtie to create a merged gtf file, using all the files I want to compare in the DEG analysis. After that I have use featureCount to create the count matrix, and as featureCount uses gtf file "geneid" by default, in the result count table, I have a very big list of MSTRG------ named genes. I would like to know if using an option in featureCount gives the posibility to change from geneid to refgeneid that is the ENSMBLE ID.

Maybe -g < string > (GTF.attrType), option and ther use "refgeneid"? Would this change be correct? Or maybe I have realized now that there is another option named −−extraAttributes < string > (GTF.attrType.extra) and I can add there refgeneid?

Thanks in advance,

Iraia

ADD COMMENTlink modified 9 months ago by Wei Shi3.2k • written 9 months ago by IRAIA.MAIALEN0
Answer: How to change stringtie gene_id names with ref_gene_id when performing featureCo
2
gravatar for Wei Shi
9 months ago by
Wei Shi3.2k
Australia
Wei Shi3.2k wrote:

If "refgeneid" is included as an attribute type in your GTF file, you can set GTF.attrType="refgeneid" to instruct featureCounts to count reads to this type of genes.

The parameter "GTF.attrType.extra" does not work for this purpose. It just extracts extra annotation data from your gtf file and adds them to featureCounts output.

ADD COMMENTlink written 9 months ago by Wei Shi3.2k
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