Tophat-Cufflinks small sample

[GermanGrekhov]

Hello.

Does anybody use Tophat-Cufflinks for RNA sequencing analysis?
I want to know how to use these tools but I can not find any small datasets which give some correct results.

I have tried to run Tophat with test_data from their site but it is only one very small sample and Cufflinks gives only empty results for this input data.

When I try to find a bigger data then it is usually some 1.5-2 Gb of short-reads, and it is handled too long. But I want to see some very small examples which gives non-empty results.

Could you share with me some small test datasets for the tools, please?

[Bukowski]

There's plenty of data from the Sequence Read Archive that you could use:

http://www.ncbi.nlm.nih.gov/sra

If you don't want to use a full dataset, then you can just subsample the reads from a larger experiment. I find for testing though doing a full analysis then extracting a bunch of reads from a subset of genes you know to be differentially expressed is a good way to create a small dataset that will give you results whilst you're testing software.

[GermanGrekhov]

There's plenty of data from the Sequence Read Archive that you could use:

http://www.ncbi.nlm.nih.gov/sra

If you don't want to use a full dataset, then you can just subsample the reads from a larger experiment. I find for testing though doing a full analysis then extracting a bunch of reads from a subset of genes you know to be differentially expressed is a good way to create a small dataset that will give you results whilst you're testing software.

Hm, thanks a lot!
I've just cut the file from 1.5 Gb to 30 Mb and Tophat+Cufflinks pipeline gives non-empty results. Great!