Hi,
I'm trying to count exons with htseq-count, but it output zero for each exon.
no_feature 25949515
ambiguous 0
too_low_aQual 0
not_aligned 0
alignment_not_unique 8374881
Here is the command I used:
python -m HTSeq.scripts.count --stranded=no --mode=intersection-nonempty -t exon -i exon_id ensembl.human.gtf sample.sam > output
reads are aligned by tophat2, reference gtf file is from ensembl: Homo_sapiens.GRCh37.73.gtf
There are about 68648819 lines in the sam file, as the statistic revealed by htseq
no_feature 25949515
alignment_not_unique 8374881
I wondering where is the other alignments
Would anyone help me solve this problem?
Any help would be appreciated. Thank you!
I'm trying to count exons with htseq-count, but it output zero for each exon.
no_feature 25949515
ambiguous 0
too_low_aQual 0
not_aligned 0
alignment_not_unique 8374881
Here is the command I used:
python -m HTSeq.scripts.count --stranded=no --mode=intersection-nonempty -t exon -i exon_id ensembl.human.gtf sample.sam > output
reads are aligned by tophat2, reference gtf file is from ensembl: Homo_sapiens.GRCh37.73.gtf
There are about 68648819 lines in the sam file, as the statistic revealed by htseq
no_feature 25949515
alignment_not_unique 8374881
I wondering where is the other alignments
Would anyone help me solve this problem?
Any help would be appreciated. Thank you!
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