why we performed cufflinks and what does the assembled transcripts mean?

Question

[zizigolu]

Hi,

why we performed cufflinks and what does the assembled transcripts mean? I read the protocol, if I am right that cufflink will provide a reference transcriptome on which the reads can be aligned and enables use to calculate the expression level of genes???

[GouthamAtla]

Discuss with who asked you to perform cufflinks. They may have better understanding why did "you" performed cufflinks.

I am just wondering how can you ask "why we performed cufflinks" ?

[zizigolu]

she only asked me to prepare DE genes for her now asking why I did so :(

Answer 1

[Satyajeet Khare]

Cufflinks builds the transcriptome for a sample. Transcripts are assembled using aligned reads which you provide in the form of a bam file. It also quantifies the assembles transcripts. Reference transcriptome is provided if it is available for that species. It helps cufflinks in building the transcriptome of the sample.

[zizigolu]

thank you, sorry in previous post you hepled me to run tophat2 but I performed based on the code. then I performed based on which of these??? counting on unique/multi mapped reads, strand specificity, whole gene or exon based analysis?

[Ram]

You should really try to understand what you're doing and why you're doing before you do it. As we have told you multiple times, we cannot and will not do your thinking for you. Copy-pasting code is one of the worst things you can do to yourself.

[zizigolu]

why you admins don't allow another people to help me? when you fight with me like this others prefer not to read my posts :(

[Ram]

I'm glad to help you with any questions you may have, but part of growing is realizing how to ask the right questions. At your stage, you need to look at the bigger picture and focus on the science behind the process. Following instructions or doing something just because your advisor asked you to would help you in the short term, but will hinder your growth as a scientist.

I wish you and everyone here the best, and that is why I insist everyone ask why before doing anything. You deserve to know, and you deserve to know better.

[WouterDeCoster]

What makes you think people aren't allowed to help you? You need a basic understanding of what you are doing, why you do those steps and how these work. Without those, your research and results are pointless. Methods matter...

[zizigolu]

sorry I was disappointed and a bit angry and I told nonsense

excuse me

actually without biostars I could not do anything...Ram, Devon, all always help me

[Ram]

No worries. Before you post anything online, I'd recommend you compose yourself, take a few deep breaths, then re-read your post until you're sure everyone will understand the content. Hold yourself to better standards - we are all happy to watch one another grow and get better.

[zizigolu]

:( :( :( thanks again