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.


2010/12/24: This page has been revamped and expanded (the original page and data can be found here). Raw reads are now available. Processed data is also available from both cell types (originally only UESC/UNDIFF was up). The genome browser saved session has been expanded to contain all of the above (the original session is still available) and the tracks are better organized.

Our paper


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

Other appearances in press:

Our data

Our raw colorspace RNA-Seq reads and their read mappings (in BED format) should be available via GEO accession GSE24622 (make sure to read the file GSE24622_README.txt about the file format conventions). However, as of 2010/12/24, our GEO entry still does not show the raw reads (but does show the mappings), so in the meanwhile you can download the raw reads from us:

See the table in the Supplement to our paper for detailed information about each barcode.

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-e (using approximately the same display conventions), except that the session shows data from both UESC and Neural precursor cells for each track, and also separates the wiggle-format data into plus and minus strand tracks. The session also shows the actual read mappings (although in many cases, there are too many reads for the browser to display). There are very many tracks, so loading might be slow as you navigate around the genome.

If the above saved browser session doesn't work, copy-and-paste these URLs into the "Add Custom Tracks" box (these are either small or they are bigBed/bigWig-format tracks, so they should get added fast, although subsequent navigation may be slow).

Software releases

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.

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