[BioC] deqseq_count and BWA-based SAM files

[Wyatt McMahon [guest]]

Hello all, 

I'm trying to use DEXSeq to identify and quantitate alternative splicing events following transgene expression.  I've used BWA to map my reads and now have the resulting SAM files.  However, when I use dexseq_count (a Python script) to convert this to a ExonCountSet, I get the following error message:
"/common/groups/dac/Hawaii/my_new_env/lib/python2.6/site-packages/HTSeq/__init__.py:592: UserWarning: Read HWUSI-EAS381R:1:10:12324:1388#CGATGT claims to have an aligned mate which could not be found. (Is the SAM file properly sorted?)"

I can see that my SAM file is not "sorted" properly.  Does anyone have a workaround for this?  I've searched all over and all I can find is people writing, "I used a perl script as a workaround."

Thanks in advance,

Wyatt

 -- output of sessionInfo(): 

R version 2.14.0 (2011-10-31)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=C                 LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] DEXSeq_1.0.2   Biobase_2.14.0

loaded via a namespace (and not attached):
[1] hwriter_1.3    plyr_1.6       statmod_1.4.14 stringr_0.6


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