Dear BioStars community,
I have paired-end (150bp) data for the chicken Ileum from Illumina TruSeq. I was told that it is first stranded. I removed the adapters through Trimmomatic tool. I then aligned it to the Chicken Genome (Ensembl) galGal4 using STAR aligner as well as Tophat2.
I wanted to quantify the reads using htseq-count, so I sorted the bam file by name with samtools sort.
I used the following parameters for htseq-count :
htseq-count -f bam -r name -s reverse -t exon -i gene_id -m union Sample15_STAR.sorted.bam Gallus_gallus.Gallus_gallus-5.0.86.gtf > Sample15_STAR_HTSeq_samout
At the end approx. 33600000 SAM alignment pairs were processed. The problem is that I get therefore a very high number of no feature.
Can anybody tell me, what is the problem?
Thanks a lot in advance! fibi_prog_omics