Closed sylvainforet closed 10 years ago
Thanks! I'll apply this patch in the next version release. In the meantime...
The authors recommend using IGV to view the output.
http://www.broadinstitute.org/igv/
Just import the assembly, bam and ALE scores. You can convert the .ale file to a set of .wig files with ale2wiggle.py and IGV can read those directly. Depending on your genome size you may want to convert the .wig files to the BigWig format.
The internal, debugging plotter is not in active development and is no longer supported.
Thanks for developing ALE, very useful! Here is a trivial patch that make the plotting of single contigs considerably faster: