Hi all,
I'm using htseq count and fortunately, I didn't get any error. However, what concerns me most is the no feature and the alignment not unique options. They've been given me headache. They are just very high.
I used the following code:
htseq-count -m intersection-nonempty -s no -i gene_ id infile.sam genes.gtf > outfile.txt.
my first sample gave:
No feature 7411932
ambiguos 26682
too low aquality 0
not aligned 0
alignment not unique 32980337
for my second sample:
No feature 7024086
ambiguos 28678
too low aquality 0
not aligned 0
alignment not unique 9537858
I got my genes.gtf from the igenome ensembl. The reads from the first sample is ~48million while for the second is ~50 million. I used tophat2 for the alignments. Please help...I'm stuck.
My second question : at what count statistics is it optimal to be used in DESeq?
Thanks.
I'm using htseq count and fortunately, I didn't get any error. However, what concerns me most is the no feature and the alignment not unique options. They've been given me headache. They are just very high.
I used the following code:
htseq-count -m intersection-nonempty -s no -i gene_ id infile.sam genes.gtf > outfile.txt.
my first sample gave:
No feature 7411932
ambiguos 26682
too low aquality 0
not aligned 0
alignment not unique 32980337
for my second sample:
No feature 7024086
ambiguos 28678
too low aquality 0
not aligned 0
alignment not unique 9537858
I got my genes.gtf from the igenome ensembl. The reads from the first sample is ~48million while for the second is ~50 million. I used tophat2 for the alignments. Please help...I'm stuck.
My second question : at what count statistics is it optimal to be used in DESeq?
Thanks.
Comment