This is the Windows app named Altrans whose latest release can be downloaded as altrans.v1.1.02.windows.x86.zip. It can be run online in the free hosting provider OnWorks for workstations.
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Altrans
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DESCRIPTION
Altrans is a method for the relative quantification of splicing events. It requires a BAM alignment file from an RNA-seq experiment and an annotation file in GTF format detailing the location of the exons in the genome. It uses paired end reads where one mate maps to one exon and the other mate to a different exon and/or split reads spanning exon exon junctions to count “links” between two exons. When there are overlapping exons, these are grouped into “exon groups” and unique portions of each exon in an exon group are identified which are used when assigning reads to an exon. The link counts ascertained from unique regions are normalized with the probability of observing such a link given the insert size distribution which is referred to as link coverage. Finally the quantitative metric produced is the fraction of one link’s coverage over the sum of the coverages of all the links that the initial first exon makes.
Audience
Science/Research
Categories
This is an application that can also be fetched from https://sourceforge.net/projects/altrans/. It has been hosted in OnWorks in order to be run online in an easiest way from one of our free Operative Systems.
