Contains a library of scripts used frequently
merge_counts_data.pyWhat: after running featureCounts or salmon for each individual, we would like to merge the count from each individual into a file for downstream processing, such as running differential gene expression. Usage:
- This script takes in:
--type: indicates whether it'sfeatureCountsorsalmon--sample_list: this is a space delimited file where the first column is the sample name and the second column is the full path to the count file for that sample--outfile: this is the path to the output file. The number of column in this output file is equal to the number of individuals (number of rows) in the sample_list file.