/mnt/max/b/genomics_facility/DKlab/mr/tzanos/rep/rMATS Dimitris Tzanos Wed, Apr 29, 2020 at 4:00 PM To: Martin Reczko Good evening Martin, I hope this email finds you well. Are you eagerly looking forward to returning to our working place this Monday, after lifting the restrictions? I try to keep pace with your work, but I still have a few questions I would like to ask. Firstly, a question of theoretical nature. I see you make use of cutadapt to remove the adapter sequences. Are these sequences provided to you by dr. Kontoyiannis? Are they the default sequences in use for these technologies? Reading your code and trying to make myself familiar with this sort of analysis I run into the awk command and .awk files. Is this the native command for pattern matching from these given files in UNIX/Linux systems? In the same block of code there is a reference to some Nature Protocol. Is that what you follow? How can I search for it? In the code for DE genes of total RNAseq analysis you utilise 'psych' package. Is it the toolbox for Psychological research? Have you run the code? I only have edgeR output for a total RNAseq of 0 hours treatment. Shall I try to run the rest of the code? I really am sorry to bother you that often,I hope that after the strict timeline dr.Kontoyiannis has set expires, I will have the flexibility to pay more time on training on my own. Again thank you for your aid and patience. Best regards, Dimitris Tzanos