--- a/README.markdown Sat Feb 08 11:35:59 2020 -0500
+++ b/README.markdown Sun Feb 09 13:23:50 2020 -0500
@@ -556,3 +556,61 @@
At this point I just gave up on using Unicode at the REPL and created `.gp`
files that I then `load`. The GPL strikes again.
+
+## 2020-02-09
+
+Installed R Studio from the `.deb`. Needed to `apt install r-base` first to get
+the dependencies. It installed… a lot of stuff. Let's hope it hasn't wreaked
+too much havoc.
+
+Moved on to differential gene expression with `cuffdiff`. Finally starting to
+understand what the actual data files are. The input FASTQs are:
+
+ GSM794483_C1_R1_1.fq.gz
+ GSM794483_C1_R1_2.fq.gz
+ GSM794484_C1_R2_1.fq.gz
+ GSM794484_C1_R2_2.fq.gz
+ GSM794485_C1_R3_1.fq.gz
+ GSM794485_C1_R3_2.fq.gz
+ GSM794486_C2_R1_1.fq.gz
+ GSM794486_C2_R1_2.fq.gz
+ GSM794487_C2_R2_1.fq.gz
+ GSM794487_C2_R2_2.fq.gz
+ GSM794488_C2_R3_1.fq.gz
+ GSM794488_C2_R3_2.fq.gz
+
+The `C` here apparently stands for "condition". I still have no idea what
+`R[123]` is trying to tell me. The `_[12]` is the paired-end read pairs. Would
+it kill people to name things more descriptively and/or include a `README` that
+explains what all their one-letter abbreviations mean?
+
+Thinking about restructuring the filesystem layout to make the relationships
+between the FASTQ files more explicit:
+
+ C1/
+ R1/
+ GSM794483_C1_R1_1.fq.gz
+ GSM794483_C1_R1_2.fq.gz
+ R3/
+ GSM794484_C1_R2_1.fq.gz
+ GSM794484_C1_R2_2.fq.gz
+ R3/
+ GSM794485_C1_R3_1.fq.gz
+ GSM794485_C1_R3_2.fq.gz
+ C2/
+ R1/
+ GSM794486_C2_R1_1.fq.gz
+ GSM794486_C2_R1_2.fq.gz
+ R2/
+ GSM794487_C2_R2_1.fq.gz
+ GSM794487_C2_R2_2.fq.gz
+ R3/
+ GSM794488_C2_R3_1.fq.gz
+ GSM794488_C2_R3_2.fq.gz
+
+But I might be too lazy at this point to do it.
+
+The more I work with `make` the more I realize how limited it is. The general
+idea behind it (computing a dependency graph and using it to rebuild things) is
+sound, but the implementation is a clusterfuck of string processing and horrific
+syntax. It really gives me the urge to create Yet Another Build System. Sigh.