Question: why we performed cufflinks and what does the assembled transcripts mean?
1
gravatar for A
4.2 years ago by
A3.9k
A3.9k wrote:

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???

rna-seq • 1.2k views
ADD COMMENTlink written 4.2 years ago by A3.9k

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" ?

ADD REPLYlink modified 4.2 years ago • written 4.2 years ago by geek_y11k
1

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

ADD REPLYlink written 4.2 years ago by A3.9k
3
gravatar for Satyajeet Khare
4.2 years ago by
Satyajeet Khare1.6k
Pune, India
Satyajeet Khare1.6k wrote:

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.

ADD COMMENTlink modified 4.2 years ago • written 4.2 years ago by Satyajeet Khare1.6k
1

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?

ADD REPLYlink written 4.2 years ago by A3.9k
2

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.

ADD REPLYlink written 4.2 years ago by _r_am31k
1

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 :(

ADD REPLYlink modified 4.2 years ago • written 4.2 years ago by A3.9k
1

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.

ADD REPLYlink written 4.2 years ago by _r_am31k

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...

ADD REPLYlink written 4.2 years ago by WouterDeCoster44k
1

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

ADD REPLYlink modified 4.2 years ago • written 4.2 years ago by A3.9k
1

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.

ADD REPLYlink written 4.2 years ago by _r_am31k

:( :( :( thanks again

ADD REPLYlink written 4.2 years ago by A3.9k
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