In version 2.0.5 we fixed some issues that were causing problems related to exon analysis. Are you using this version.
If you are using this version, then it could be an issue with the bed files or something else. To test this, you can try the sample data in our tutorial:
If this works fine for you then it could be the bed file or the way the samples are named. For more on creating the exon bed file see:
bamToBed -i accepted_hits.bam -split| coverageBed -a stdin -b /home/user/BAMtoBED/hESC_differentiation_exons.bed > /home/user/RNASeqStudy/Sample1/day0_s1__exons.bed
For more on the file naming conventions see:
Finally, you can simply assess the quality of the bed file by looking at the read counts associated with exons in genes you know should be highly expressed and genes you know are not expressed based on the junction data (you can search for the Ensembl gene IDs in this file).
On Dec 7, 2011, at 8:21 AM, Zhang Yijing <yz...@partners.org> wrote: