pipelines

Pipelines for processing a batch of files automatically. All the scripts were required Python 3.x.

main_salmon

Using salmon to process the RNA-seq data, obtaining TPM value of each gene.

• single_ended.py: This program is used for processing the single ended sequencing data
• for the paired-ended sequencing data, use main_salmon.py
• for merging the results of salmon, using main_merge_data.py
• The detailed infomation of how to use the programs, just type the conrespondance names of scripts plus "--help".

bwa_proc

In the bwa_proc dictionary, it contains all the bwa_sention process. For how to use the program, just copy correspondance file to the dictionary that contains the files you want to process. And type python $your_program.