I'm trying to extract counts for each gene from the sorted.bam file using htseq-count. But I end with an error. Command I used:
htseq-count –s reverse –f bam –q sample.sorted.bam gencode.v27.primary_assembly.annotation.gtf > sample1_counts.txt
I have this error:
/path/soft/apps/HTSeq/0.6.1p1-goolf-1.7.20-Python-2.7.11/bin/htseq-count: Error: Please provide two arguments. Call with '-h' to get usage information.
For aligning reads to the genome I used Hisat2 tool. I didn't use any gtf file here. Following is the hisat2 command I used:
hisat2 -p 8 --dta --rna-strandness RF -x /grch38_snp_tran/genome_snp_tran -1 sample.1.fastq.gz -2 sample.2.fastq.gz | samtools view -Sb - > sample.bam; samtools sort -T /tmp/sample.sorted -o sample.sorted.bam sample.bam
Did I go wrong with the alignment step? Why htseq-count is showing the Error?