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  • dexseq_count.py vs htseq-count

    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
    Last edited by Petros84; 10-17-2014, 06:59 AM.

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