The most recent version of EaSeq (v. 1.03) got a new ‘Beta-panel’ (download here).
It can be found in the right side of the Labdesk, below the button for the Navigation panel, and so far it contains a couple of new tools:
The ‘Get Sequences’-tool.
This tool downloads genome sequences (requires some GBs of disk space) from UCSC and export the sequences from a regionset. This is useful if you would like to generate input data for motif finding at a set of peaks e.g. using the Meme suite. When doing so it is good practice to also generate a set of negative control regions. You can use the ‘Controls’-tool for that. It will generate a set of random regions that correspond to your peaks, and if you instruct it to match the control regions to a Regionset containing TSS, then they will on a population level be at the same distance and orientation to TSS as the peaks.
The ‘Locus crawler’-tool.
This tool will help you imaging the signal at a list of individual loci. You will first need to make some tracks of the datasets you would like to visualize, and then paste the list of coordinates, gene names, or accession number for the loci that you would like to have visualized. When running the tool, it will create snapshots of all the loci. It can be quite a time save compared to genome browsing the loci manually.
Tools in the beta-panel are still under development, so use them with care. But we thought that it would be useful to get user feedback before finalizing them. EaSeq is made for you, so please do report back whether the tools function as intended or not – or if you have suggestions for additions or changes in general.
We have several other tools that also mostly ready for primetime, and will add them to the ‘Beta-panel’ in the upcomming releases, evaluate your feedback, and integrate them further into EaSeq at a later time, when a major make-over of the user interface is due.v1.04: PDF export and other plot improvements ChIP-seq data analysis workshop on April 12