Dear Capricy Gao,

Let me know if I am wrong, but it sounds like you are using a vignette 
found by google that does not match with the version of DEXSeq that you 
are using.  What version of DEXSeq do you have installed?

The "-r" option was included from DEXSeq 1.7.8, so first make sure that 
you have this or a newer version installed.

Best regards,
Alejandro

> I am planning to compare the exon usage between samples. This is my first time to use Dexdeq. The problem came when I tried to use dexseq_count.py.
>
>
> My RNAseq data was mapped using tophat, then  the bam file was samtools sorted with -n (by name) , samtools converted the sorted bam into sam
>
> I followed the online manual (http://www.bioconductor.org/packages/2.13/bioc/vignettes/DEXSeq/inst/doc/DEXSeq.pdf) to fun dexseq_count:
>
> /R/x86_64-pc-linux-gnu-library/2.15/DEXSeq/python_scripts/dexseq_count.py  -r name -p yes -s no HTseqFormat_flatterned.gff sample.sam sample.exonCounts
>
>
> the first error message was :  no such option: -r
>
> Could anybody let me know why? On page 5 of the manual, it clearly says this option should be included
>
>
> I then deleted this option and a lot of warnings came out:  claims to have an aligned mate which could not be found. (Is the SAM file properly sorted?)
>
> These warnings might came up because when I ran tophat, I did not specify the correct " expected (mean) inner distance between mate pairs". I wonder if I could just remove -p option and treat the file like non paired-end data?
>
>
> Thanks a lot:)
>
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