I am writing to you regarding some issues with vector_analyze.py.
In line 387, the code reads vector_insertion = pd.read_csv(directory_store+“/”+basename + “_vector_confident_inser.tab”, sep = ‘\t’). However, it seems that the confident_inser.tab file is not being generated. I assume that this file is a subset of the ‘vector_baitonly_inser.tab’ file with the Type=Confident designation. Can you confirm if my understanding is correct?
During this step, the unique/*SID_all_dsb.tab file is required. However, it appears that PEM-Q.py does not generate this file, but rather the result/*Translocation_dsb.tab file. Could you please clarify if the result/*Translocation_dsb.tab file is the correct one to use? Additionally, could you explain the meaning of dsb in this context?
Furthermore, in line 127, the code bwa mem -t 8 -k 10 /home/mengzhu/database/bwa_indexes/{}/{} {} contains the unnecessary part /home/mengzhu/database/bwa_indexes/. It should be removed.
Thank you for your attention to these matters. I appreciate your prompt response.
Dear Mengzhu,
I am writing to you regarding some issues with vector_analyze.py.
In line 387, the code reads
vector_insertion = pd.read_csv(directory_store+“/”+basename + “_vector_confident_inser.tab”, sep = ‘\t’). However, it seems that theconfident_inser.tabfile is not being generated. I assume that this file is a subset of the ‘vector_baitonly_inser.tab’ file with theType=Confidentdesignation. Can you confirm if my understanding is correct?During this step, the
unique/*SID_all_dsb.tabfile is required. However, it appears that PEM-Q.py does not generate this file, but rather theresult/*Translocation_dsb.tabfile. Could you please clarify if theresult/*Translocation_dsb.tabfile is the correct one to use? Additionally, could you explain the meaning ofdsbin this context?Furthermore, in line 127, the code
bwa mem -t 8 -k 10 /home/mengzhu/database/bwa_indexes/{}/{} {}contains the unnecessary part/home/mengzhu/database/bwa_indexes/. It should be removed.Thank you for your attention to these matters. I appreciate your prompt response.
Best regards, Yang