mirimia
commented
6 years ago This hasn’t worked well, even for the KD0. Either a problem in your config or output folder. Can you copy paste an ls of the to_combine/ folder?
I can’t access the config from here. Andre, could you please take care of this?
Hello, I am trying to use the merge function to combine replicates of experimental conditions, prior to the combine step. I have attached my config file, where I specify the merging of three replicates per experimental condition. I have pasted my command and the output below. It seems like only one condition was merged, while the remainder were not. Why is this? It seems to begin with the file KD_0A_R1, but then the merged output is KD_0B...
Also, once they are merged, do I need to move them to a new directory for the combine step, to be sure only the merged files are combined?
Thanks in advance, Brian
/n/scratch2/btk4/VAST/vast-tools/--[ 180423_12:40:21 ]==> /n/scratch2/btk4/VAST/vast-tools/vast-tools merge --groups config_file.txt [vast merge]: Setting output directory to /n/scratch2/btk4/VAST/vast-tools/vast_out [vast merge]: KD_0A_R1: found to_combine/KD_0A_R1.info. Sample will be treated as being strand-specific. [vast merge]: Loading IR files (version 2) [vast merge]: Processing to_combine/KD_0A_R1.IR2 [vast merge]: Loading IR.summary_v2.txt files [vast merge]: Processing to_combine/KD_0A_R1.IR.summary_v2.txt [vast merge]: Loading Microexon files [vast merge]: Processing to_combine/KD_0A_R1.micX [vast merge]: Loading eej2 files [vast merge]: Processing to_combine/KD_0A_R1.eej2 [vast merge]: Loading EXSK files [vast merge]: Processing to_combine/KD_0A_R1.exskX [vast merge]: Loading MULTI files [vast merge]: Processing to_combine/KD_0A_R1.MULTI3X [vast merge]: Printing group files [vast merge]: >>> KD_0KD_0B_R1
config_file.txt