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bioinformatics-core-shared-training / rnaseq-pipeline

A Short Course on the interpretation of results from the CRUK-CI rna-seq pipeline
https://bioinformatics-core-shared-training.github.io/rnaseq-pipeline
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Datasets #1

Closed markdunning closed 7 years ago

markdunning commented 8 years ago

Decide on dataset(s) we can use in the course

gdbzork commented 8 years ago

Actually this was going to be Rory's task, I thought.

markdunning commented 8 years ago

I thought that both you and Rory would be looking into it. But now I remember we decided that Rory was going to have the initial look.

Here is the publication for the dataset I mentioned in the meeting:-

Transcriptional profiling of the epigenetic regulator Smchd1

GSE64099 R workflow

I grabbed the fastq files from SRA: SRP051084

And here they are here on lustre:-

/lustre/mib-cri/dunnin01/rna-seq-example/GEO/fastq/

However, running the pipeline only gives 3 DE genes compared to the 1000s I get following their analysis. Since it's the first time I've run the pipeline I guess I could have done something wrong

gdbzork commented 8 years ago

Well, the pipeline as is leaves much to be desired... I'll try it on the new one I'm working on. Thanks for passing it along, anyway.

markdunning commented 8 years ago

GEO entry for Hisham's data?

http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE68358

rorystark commented 8 years ago

Yea these are them

Sent from phone

On Sep 14, 2016, at 16:21, Mark Dunning notifications@github.com<mailto:notifications@github.com> wrote:

GEO entry for Hisham's data?

http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE68358

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