Question

example fastq file, sampleAnnotaition and Hairpin file for shRNAseq/EdgeR tool

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@k-8495

Last seen 22 months ago

United States

Hello,

I am interested in trying out a tutorial with example data using the shRNAseq tool (which has been integrated into EdgeR) . The tutorial is here: http://bioinf.wehi.edu.au/shRNAseq/pooledScreenAnalysis.pdf.

There are some example data files here: http://bioinf.wehi.edu.au/shRNAseq/, but are taking forever to download.

I was wondering if these shRNAseq example fastq files are available as part of the Bioconductor package, or already loaded to galaxy.

Thanks,

K

shRNAseq edgeR shRNA • 2.9k views

ADD COMMENT • link updated 9.2 years ago by Gordon Smyth 51k • written 9.2 years ago by KB ▴ 50

score 0 · Answer 1 · 2015-09-22

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@k-8495

Last seen 22 months ago

United States

Took me a long time, but I was finally able to download an example file from here: http://bioinf.wehi.edu.au/shRNAseq/

ADD COMMENT • link 9.2 years ago KB ▴ 50

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Some of the files are pretty big, so depending on your connection and location, it's not surprising that it takes a while. I don't think that putting them into a Bioconductor package would make the download any smaller.

ADD REPLY • link 9.2 years ago Aaron Lun ★ 28k

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Thank you.

So I am trying out example with screen2.fastq, samples2.txt and hairpins2.txt (obtained from screen2.tar.gz located http://bioinf.wehi.edu.au/shRNAseq/) and followed instructions here: http://bioinf.wehi.edu.au/shRNAseq/galaxy.html. I get this error.

Error in locfitByCol(loglik, covariate, span = span, degree = 0) : 
  locfit required but is not available
Calls: estimateDisp -> WLEB -> locfitByCol
Execution halted

Could you help figure out what the issue is ? Thank you

ADD REPLY • link 9.2 years ago KB ▴ 50

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You need to install locfit. Try biocLite("locfit"). It's only a suggested package for edgeR, so it doesn't get installed automatically when you install edgeR.