2017.12.01

After the first seminar yesterday (30.11) the group met again to discuss the progress that has been made so far. Arif has made a preliminary script that mapped all the transcripts onto the reference genome which we got from Ensembl. The idea of filtering all these data based only on the protein-coding genes was tabled and agreed. A to-do list that we agreed to achieve by the end of the week is as follows:

• Combine metadata and raw counts → patient code vs gene codes.
• Look up whether to sum up or take median/mean for the samples that were sequenced multiple times (deeper coverage).
• Get information regarding the workflow so far up until we get the raw count.
• Upload reference regarding TPM value cut-off.

Once these are done, we can then continue with the differential expression analysis, with heavy emphasis on the statistics. :)
The group also welcome a new member. This afternoon (01.12), I will brief him regarding what has been done so far and what the group will try to do in the immediate future.
I am still a bit bummed because I have not contributed much to the scripting part due to the scheduling complication with another course. Hopefully, I will be able to contribute a bit more stuff soon...