RNA BULK SEG ANALYSIS

Question

[IMDAD_PBG]

Currently, I am doing RNA bulk seg analysis for two pools the tolerant and sensitive, after performing RNA sequencing analysis which software or method of association should I use for identification of candidate loci of tolerant and sensitive genomic regions

[andrew.j.skelton73]

The term you're looking for is differential expression. There's lots of tools out there, but generally Limma Voom, or DESeq2 are the packages of choice. In future, members of the community will be a lot more receptive if you've shown some effort in trying to answer the question yourself. There are lots of posts on biostars surrounding the topic of differential expression, such as Q: What is Differential Expression

Answer 1

[ATpoint]

Spend some quality time on reading this quiet comprehensive RNA-seq workflow, covering the essential points.

[IMDAD_PBG]

thanks. can you recommend me some more specific methods used in RNA bulk seg analysis in wheat for identification of genes of tolerence?

[ATpoint]

No, because I have no idea what your exact scientific question is. Please point out the experimental setup and the exact question you want to answer. Then we'll see where to direct you =)

[Kevin Blighe]

Good work dude!

[IMDAD_PBG]

we want to identify gene/genes for resistance in wheat. we have chosen 10 resistance and 10 sensitive wheat cultivars form a wheat population. we did RNA-BSR of two pools. now we have sequences of both pools. so how to find gene/loci of tolerance and sensitivity associated? which software or analysis need to use to identify the gene/genomic regions?

[IMDAD_PBG]

we want to identify gene/genes for resistance in wheat. we have chosen 10 resistance and 10 sensitive wheat cultivars form a wheat population. we did RNA-BSR of two pools. now we have sequences of both pools. so how to find gene/loci of tolerance and sensitivity associated? which software or analysis need to use to identify the gene/genomic regions?