dexseq_count.py vs htseq-count

[Petros84]

Dear All,

I have some RNA paired-end files which I have used tophat to allign

~/tophat-2.0.7.Linux_x86_64/./tophat -p10 --segment-length 18
--no-coverage-search --segment-mismatches 1 -G

then samtools

samtools sort -n /media//PRE_6_8_2/accepted_hits.bam
/media/PRE_6_8_2/PRE_6_8_2.sort.hg19.bam

and then

samtools view /media/PRE_6_8_2/PRE_6_8_2.sort.hg19.bam.bam
/media/PRE_6_8_2/PRE_6_8_2.sort.hg19.sam

then I am trying to use DEXSeq and using the

python2.7 /home/3.0/DEXSeq
/python_scripts/dexseq_count.py -p yes -r name -s no
/media/PRE_6_8_2/hg19/hg19_IlluminaAnnotation_genes.gtf
/media/PRE_6_8_2/PRE_6_8_2.sort.hg19.sam
/media/PRE_6_8_2//PRE_6_8_2/untreated1fb.txt

and gives me

_ambiguous 0
_empty 39845364
_lowaqual 0
_notaligned 0

without any reads for any exons. 0 for everything

whereas by using the htseq-count -r name -s no everything looks fine (reads in genes)...

could you please advice me how to solve it? I really need to run the DEXseq as I want reads per exon to detect splice differences.

Thank you in advance for your help