Does anyone know how to use htseq-count with several samples ?
We can use htseq-count like : htseq-count sample1.sam reference.gtf > result.count.txt
We can get sample1's count data by above command. But, it is usual that we have more than two sample. So, we have to run htseq-count for each sample's sam file. Do many people combine result matrix after running each htseq-count by sample ? or Can we make expression matrix with several samples at the same time ?
Also, I think there is some difference between samples like total expression amount or reads number. How many people do any normalization or correction between samples ?