FragSeq

WARNING: This is an outdated archive page. The current page is here.

This page is the main source of information about FragSeq. Future releases, updates, and patches of FragSeq software, as well as improved documentation, will be available through this page.

Our paper

Reference:

• Underwood JG*, Uzilov AV*, Katzman S, Onodera CS, Mainzer JE, Mathews DH, Lowe TM, Salama SR, Haussler D. FragSeq: transcriptome-wide RNA structure probing using high-throughput sequencing. Nature Methods 7, 995–1001 (2010).
  • Starred (*) authors contributed equally to this work.

In that paper, version 0.0.1 of the software was used, which you can download below.

Other appearances in press:

• Covered by a "News and Views" story by Eric Westhof and Pascale Romby, Nature Methods 7, 965–967 (2010).
• A CBSE news story about FragSeq.

Our data

Our raw colorspace RNA-Seq reads and their read mappings (in BED format) are available via GEO accession GSE24622 (make sure to read the file GSE24622_README.txt about the file format conventions).

Here are all the files (zip archive or gzipped tarball) that our software output when running the analysis. Or you could just run it yourself, it's easy (see the README.txt file in the version 0.0.1 release below).

If you want to see our data in the UCSC Genome Browser, use this genome browser saved session. The tracks in it correspond to data shown in paper Fig 2a,c-e. If it doesn't work, copy-and-paste the following URLS into the "Add Custom Tracks" box (only UESC samples shown):

http://users.soe.ucsc.edu/~auzilov/FragSeq/rnas.bed
http://users.soe.ucsc.edu/~auzilov/FragSeq/undiff.rawends.minus.ss.track
http://users.soe.ucsc.edu/~auzilov/FragSeq/undiff.rawends.minus.ssbg.track
http://users.soe.ucsc.edu/~auzilov/FragSeq/undiff.rawends.plus.ss.track
http://users.soe.ucsc.edu/~auzilov/FragSeq/undiff.rawends.plus.ssbg.track
http://users.soe.ucsc.edu/~auzilov/FragSeq/undiff.probs.minus.ss.track
http://users.soe.ucsc.edu/~auzilov/FragSeq/undiff.probs.minus.ssbg.track
http://users.soe.ucsc.edu/~auzilov/FragSeq/undiff.probs.plus.ss.track
http://users.soe.ucsc.edu/~auzilov/FragSeq/undiff.probs.plus.ssbg.track
http://users.soe.ucsc.edu/~auzilov/FragSeq/undiff.cutscores.minus.ss.track
http://users.soe.ucsc.edu/~auzilov/FragSeq/undiff.cutscores.plus.ss.track

Software releases

• Version 0.0.1 (zip archive) (gzipped tarball)
  • This is the version used for our 2010 Nature Methods paper, and is also distributed as Supplementary Software with that paper, except the README.txt file is updated a little. This version contains config files and a script to reproduce our analysis, but you'll have to download the read mappings from GEO (see the README.txt file).

Bugs? Comments? Feature requests? Need help?

This page and software are maintained by me, Andrew Uzilov. Please contact me with any bug reports, feedback, to ask for help, and so forth.