# HG changeset patch # User Steve Losh # Date 1581272630 18000 # Node ID 0ea44182db8ae33eefb0171920f4abd6e925a251 # Parent 354ef30543e632908fa968c1ebd3fb6e0546ea3b Update diff -r 354ef30543e6 -r 0ea44182db8a README.markdown --- 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.