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
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