Dear all,

I was wondering if there is any tool to calculate PSI from the BAM files. Basically what I want is-

<img alt="" src="http://bioinformatics.oxfordjournals.org/content/29/2/273/F1.large.jpg" style="height:121px; width:500px" />

I have gtf file with all the exons and I want to calculate for each exon (lets take exon filled with grey for example) how many reads mapped to junction of that exon (a and b in figure) and how many reads skip that exon (c in figure). So if we have, let's say, 10k exons in the gtf, the output should contain 10k rows with a,b and c as columns.

I used [MATS][1] and [bam2ssj][2] but did not get what I was expecting. I have gtf file with approx. 300k exons but MATS gives the output only for 3k exons. bam2ssj is calculating the values for introns rather than exons.

Any suggestions?

Thanks in advance.

 [1]: http://rnaseq-mats.sourceforge.net/user_guide.htm
 [2]: https://github.com/pervouchine/bam2ssj
<p>I just tried to write something for this: https://github.com/lindenb/jvarkit/wiki/Biostar103303</p>

<p>I don&#39;t have any data to test though.</p>
