Question: what data normaly you use for analysis and how
0
gravatar for Learner
2.5 years ago by
Learner 220
Learner 220 wrote:

I don't have access to the raw files. I have access to the

htseq-count 
FPKM
FPKM-UQ

I have read all the questions asked in here. However, I still cannot find a good solution to the following questions

1- I want to find up and down-regulated genes, which package normally do you use and how do you convert them to the gene names?

2- which one of the above files are more reliable ? do you have any publication to refer to?

3- They come from TCGA, however, I cannot get the raw RNA seq and that is why I am trying to do the analysis based on one of the above files.

Thanks

rna-seq • 731 views
ADD COMMENTlink modified 2.5 years ago by WouterDeCoster44k • written 2.5 years ago by Learner 220

If you can't or don't want to download raw data then you could use one of the TCGA data portals to get what you need. LinkedOmics is one option.

ADD REPLYlink written 2.5 years ago by genomax85k
2

@genomax what is wrong with using htseq-count ? do you think it will not be a good idea to use that ? I personally think one can simply use that instead re-analysing the whole raw files (because you dont need to go trough splicing, alignment etc etc.

ADD REPLYlink modified 2.5 years ago • written 2.5 years ago by Mo920
2

Sure that is the best option. There would still be some effort required on @Learner's part to use/analyze the raw counts. If the aim here is casual analysis then I was suggesting a web based alternative that will be simple(r) to use.

ADD REPLYlink written 2.5 years ago by genomax85k
0
gravatar for WouterDeCoster
2.5 years ago by
Belgium
WouterDeCoster44k wrote:

Differential expression analysis is typically done using edgeR or DESeq2, for which you need the raw counts (from htseq-count). Have a look at this workflow to get started: Bioconductor RNA-seq workflow: gene-level exploratory analysis and differential expression.

and how do you convert them to the gene names?

Convert what to gene names?

ADD COMMENTlink written 2.5 years ago by WouterDeCoster44k

@WouterDeCoster I am really sorry but this is not what I am looking for. There are 100 similar posts available. Please look at the right side of this post as an example. I am more searching to learn and not just ask random questions. So if you want a upvote, you should provide a solution or detailed answer. I appreciate the time you put but please consider that one answer should lead to a learning

ADD REPLYlink written 2.5 years ago by Learner 220
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