Hello Folks,
Given all the headaches associated with BAM files, I've depreciated the
Bam2Bar app and replaced it with Sam2USeq for generating read depth coverage
tracks. Options are available for creating stranded and relative graphs.
The SAM file don't need to be sorted nor have a header. Multiple SAM files
will be merged. This app should solve some of the out of memory issues with
huge alignment files. The USeq_7.9.5 release is available from
https://sourceforge.net/projects/useq/
The xxx.useq graphs can be viewed directly in IGB or converted to wig files
with the USeq2Text app, or bigWig files with the USeq2UCSCBig app.
If you post your xxx.useq graphs to GenoPub
(http://bioserver.hci.utah.edu/BioInfo/index.php/Software:DAS2 ) you can
visualize your data in both IGB and the UCSC Genome Browser.
-cheers, D
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