Entering edit mode
3.7 years ago
hytxnt
▴
10
hi everyone ,i am a newer to ballgown ,and i am practicing the code in 《Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown 》. but i have some question when i am trying to understand it : we have a set of data, and the covariate is "sex" inculd male and femal, after the "stattest" ,we could get the "fc" vaule ,but i am confused that dose this "fc" comes from male/female or female/male ,which exactly means when fc>1, does that means male over expressed batter than female or completely converse.
if there are some function that i dont kown which lead to this question ,please reply,thank you very much.
I ask this before going into the question: Do you really want to investigate differential transcript usage rather than differential gene expression? I know the protocol you mention was published in a high impact journal and people often blindly start using it without realizing that for standard differential expression analysis on the gene level it is not the right thing to do, and there are imho better, more intuitive, computationally less expensive and especially better-documented alternatives today.
can you suggest the document ? in the gene level ? sorry to bother you ,i dont mean that ,i just want to analyse the data,and find the wanting gene . in the begining i was suggested to pactice hisat2 and stringtie ,so i searched "that" paper out .......
I understand that maybe language barrier can be a bit tricky sometimes (I and many others here are not native speakers as well) but please try to be precise. No need to apologize for anything :)
What does that mean? Do you want to know whether a gene is differentially-expressed or whether a transcript is differential?
For gene level analysis I suggest you follow this guide: https://bioconductor.org/packages/release/workflows/vignettes/rnaseqGene/inst/doc/rnaseqGene.html
i want to kown which gene is overexpressed and find the Promotor of this gene, i dont want an exact gene actually .... sorry my bad
I suggest you follow the linked workflow.
thank you so much!!! the web lock me down because i have post too much !!! ...but ... although you suggested another protocol with fresh software , i still want to know the answer of my original question ... sorry QwQ