Stringtie 计算转录组的 Raw Counts

Stringtie 自带一个脚本prepDE.py用于计算转录组的 Raw Counts，用法如下：

Usage: prepDE.py [options]

Generates two CSV files containing the count matrices for genes and
transcripts, using the coverage values found in the output of `stringtie -e`

Options:
  -h, --help            show this help message and exit
  -i INPUT, --input=INPUT, --in=INPUT
                        a folder containing all sample sub-directories, or a
                        text file with sample ID and path to its GTF file on
                        each line [default: ./]
  -g G                  where to output the gene count matrix [default:
                        gene_count_matrix.csv
  -t T                  where to output the transcript count matrix [default:
                        transcript_count_matrix.csv]
  -l LENGTH, --length=LENGTH
                        the average read length [default: 75]
  -p PA