I want to add transcripts id into DEGs results

[sdabral05]

Hi ,
I run this and its working properly .But i also want to add ENST ids .
What is understand is to change "geneNames" to the name allocated by ballgown to transcripts id in this syntax--- t_name =ballgown::geneNames(bg_chrX).
I am able to get that name .Can you please help me for this .

Code I am using -----

results_transcripts = stattest(bg_chrX, feature="transcript",covariate="Condition", getFC=TRUE, meas="FPKM")

results_transcripts = data.frame(geneNames=ballgown::geneNames(bg_chrX), geneIDs=ballgown::geneIDs(bg_chrX), results_transcripts)

[sjm042]

i am not sure ballgown can do these things

[sdabral05]

hey ,
when we use this commandfull_table <- texpr(bg_chrX , 'all') it give use total information about gene transcript id etc .
when I calculate FPKM value for transcript in data it give same number of content as present in full_table .
means - full_table if have 20 row than transcript fpkm also have 20 row and they also have same sequence of gene name so can I copy and paste the row t_name from full_table and use as tanscript name for respected FPKM value .

Its not possible that ballogown is not calculating FPKM on transcript level because feature="transcript" is all about calculation on the bases of transcript present in data that’s my understanding.

[SalmaTariq080]

Hi,
its simple just add
transcriptNames= ballgown::transcriptNames(bg)
you can add this to the code above and it will give you ENST ids