How to find gene names for csv files created by R

Question

[hirahameed222]

I have generated the csv file by using following command

write.csv(results_genes, "chrX_gene_results.csv",
      row.names=FALSE)

my output file lacks particular gene names in gene column the file appears as :

gene    MSTRG.9464  1   0.456607798602799   0.46264129580405
gene    MSTRG.61457 1   0.456608200007355   0.46264129580405
gene    MSTRG.27219 0.999999999999999   0.456608285295604   0.46264129580405

Can some one tell me that how can I find and compose particular gene names in gene in column? is there any script ? or some thing is missing in my data which fails to fetch the gene name?

[WouterDeCoster]

There is no need to SHOUT. I have removed the capital letters from your title.

It is furthermore unclear how you obtained "chrX_gene_results.csv", which is probably a crucial piece of information here.

[hirahameed222]

My Bad i haven't checked that i have All-Caps in my post. I'll care for next time. I am following this protocol for differential expression analysis, I followed the same but my results have missing gene names.

https://kimlaborg.files.wordpress.com/2017/10/nprot-2016-095.pdf

[cpad0112]

Did you furnish a reference gtf file to stringtie/cufflinks pipeline? MSRTG are temporary names given by the workflow.

[hirahameed222]

yes, I followed the protocol exactly.

[Friederike]

What's the result if, in R, you type:

head(results_genes)

[hirahameed222]

  feature              id        fc      pval      qval

1    gene ENSRNA050018849 1.4057356 0.5001672 0.5001672

2    gene ENSRNA050021620 0.8327369 0.5001672 0.5001672

3    gene         MSTRG.1 0.7915044 0.5001672 0.5001672

[cpad0112]

From your output, it seems you have reference gtf and your analysis included finding transcripts matching reference and also the novel transcripts. Wherever tool found transcripts, not in reference gtf, tool assigned MSRTG accessions to the transcripts.