Tuesday, December 10, 2013

A Reference Methylome Database and Analysis Pipeline to Facilitate Integrative and Comparative Epigenomics

Original link: http://www.plosone.org/article/info:doi/10.1371/journal.pone.0081148
DNA methylation is implicated in a surprising diversity of regulatory, evolutionary processes and diseases in eukaryotes. The introduction of whole-genome bisulfite sequencing has enabled the study of DNA methylation at a single-base resolution, revealing many new aspects of DNA methylation and highlighting the usefulness of methylome data in understanding a variety of genomic phenomena. As the number of publicly available whole-genome bisulfite sequencing studies reaches into the hundreds, reliable and convenient tools for comparing and analyzing methylomes become increasingly important. We present MethPipe, a pipeline for both low and high-level methylome analysis, and MethBase, an accompanying database of annotated methylomes from the public domain. Together these resources enable researchers to extract interesting features from methylomes and compare them with those identified in public methylomes in our database.

Examples of high-level methylation features available in MethBase through the UCSC Genome Browser track hub.

Wednesday, December 04, 2013

Convert PDF files to high quality PNG figures

To display figures on your website, it is necessary to convert PDF files to image files in PNG format. However, the conversion sometimes results in low-quality figures, especially if there are texts in the PDF original files. Below are the procedures I used to convert PDF files to high-quality PNG files. It includes two step:

1. use Preview to convert PDF files to PNG files
Open your pdf file with Preview on Mac OS. Click File->Export. Select PNG from the Format field. Below the Format selector, there is a text box Resolution, which is the key to preserve high quality. Make sure to input quite high number, say 300 pixel/inch. Click Save. This produces a png file of high quality

2. use OptiPNG to reduce PNG file size
The PNG file from the above step is usually quite big, which may make your website slow to load. The OptiPNG (http://optipng.sourceforge.net/) program can used to reduce file size. With the default settings, it is able to reduce the png file size by half without perceptible loss in image quality.

You may see a PNG figure produced with the above procedure in my MethPipe website (http://smithlab.usc.edu/methpipe/).