Question

Looking for an article with data (a few samples) and codes available !

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6.5 years ago

XBria ▴ 90

Hi everyone,

Simply, I need an article with few number of samples + codes ! (I'm gonna redo the whole research exactly the same as the article has done.)

I 've already found some. With more samples and codes and vice versa, a few samples and no codes !!

Any suggestion ?

rna-seq next-gen • 1.3k views

ADD COMMENT • link updated 6.5 years ago by WouterDeCoster 47k • written 6.5 years ago by XBria ▴ 90

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Simply,

It would be simple if you would specify a bit more what exactly you are looking for.

ADD REPLY • link 6.5 years ago by WouterDeCoster 47k

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Post is updated now.

ADD REPLY • link 6.5 years ago by XBria ▴ 90

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Rarely will you find article specific codes. RNAseq is a standard methodology now. There are a number of R packages (DESeq2, edgeR etc) that are generally used for the differential expression analysis after you align your data.

Take a look at DESeq2 vignette that includes example samples and analysis of that data.

ADD REPLY • link 6.5 years ago by GenoMax 141k

score 1 · Answer 1 · 2017-10-19

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6.5 years ago

WouterDeCoster 47k

What about this paper: Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown. (If you can't get access to that publication, let me know and I'll -cough- help you.)

ADD COMMENT • link 6.5 years ago by WouterDeCoster 47k

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Dear Wouter,

It is not accessible. can you please help me ?

Thanks,

ADD REPLY • link 6.5 years ago by XBria ▴ 90

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You can use -cough- to access any paper you want.

ADD REPLY • link 6.5 years ago by WouterDeCoster 47k

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Dear Wouter,

Your help is always useful. Anyway, I have another question about a paper below: https://link.springer.com/protocol/10.1007%2F978-1-4939-6972-2_11 The problem is that the link written in the paper is not accessible. There are down-sampled data and the rest of materials all in the mentioned website. Do you have any suggestion (maybe another link including the same data)? Since It is not possible to access the link, how can I use this paper ?

Many thanks in advance !

ADD REPLY • link 6.5 years ago by XBria ▴ 90

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It's a disgrace that a link to something that is published so recently is no longer accessible. I think the easiest way would be to contact the authors.

ADD REPLY • link 6.5 years ago by WouterDeCoster 47k

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I have already sent 3 emails to one of the authors, NO answer though !! The weird is that there is no other email address for the rest of the authors ! even on the internet !!

ADD REPLY • link 6.5 years ago by XBria ▴ 90

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Frustrating. I just contacted the first author using Twitter, let's see if that helps.

ADD REPLY • link 6.5 years ago by WouterDeCoster 47k

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Oh really !!! Many many thanks

ADD REPLY • link 6.5 years ago by XBria ▴ 90

score 0 · Answer 2 · 2017-10-19

My best suggestion: read How To Ask Good Questions On Technical And Scientific Forums. For example, do tell us which papers you found, and what you consider to be "few samples".

See if Differential analyses for RNA-seq: transcript-level estimates improve gene-level inferences suits your needs. It uses two simulated and four real datasets, and all data and code to repeat the analysis are available.