I want to count the reads using HTseq of BAM files from RNAseq aligned with TopHat. The experiment consists of 2 treated samples and 2 Untreated samples.
What is not clear to me is, Do I have to do the counting of the BAM files one by one or I can give them to HTseq altogether like I do with featureCounts?
Here is the code that I'm using
htseq-count -f bam -q -m union -s yes -t exon -i gene_id ~/RNAseq/mapping/star/Treated_1.bam Treated_2.bam Untreated_1.bam Untreated_2.bam ~/RNAseq/annotation/Homo_sapiens.GRCh37.75.gtf > /home/RNAseq/htseq-count/countReads/
and here is what I get
-bash: /home/RNAseq/htseq-count/countReads/: Is a directory
Can you kindly tell me what is wrong ?