--- a/README.markdown Thu Mar 19 20:32:36 2020 -0400
+++ b/README.markdown Tue Mar 31 16:04:42 2020 -0400
@@ -1226,3 +1226,40 @@
Crucial is still backordered. Oh well, I'll just watch more TNG while I wait
for all the alignments to complete.
+## 2020-03-31
+
+Ran the Trapnell plots from the paper on our data. Results seem at least
+plausible on the surface. Pinged my partner to see if his plots match.
+
+Attempted to install RSeQC to do the TIN score stuff mentioned in the paper.
+Ran `pip3 install RSeQC` as described in their docs, but that failed with:
+
+ ValueError: no cython installed, but can not find pysam/libchtslib.c.Make sure that cython is installed when building from the repository
+
+After some searching online I found that this can be fixed by upgrading pip with
+`pip3 install --upgrade pip`. It's… fine, I guess?
+
+Once I got it installed, I tried running `tin.py` to produce the TIN scores.
+The script wants the BAM (which I have) and a "BED" file. BED apparently stands
+for Browser Extensible Data and is a TSV file with lines like this:
+
+ chr1 67092175 67109072 XM_011541469.1 0 - 67093004 67103382 0 5 1429,187,70,145,44, 0,3059,4076,11062,16853,
+ chr1 67092175 67131183 XM_011541467.1 0 - 67093004 67127240 0 9 1429,187,70,106,68,113,158,92,42, 0,3059,4076,11062,19401,23176,33576,34990,38966,
+ chr1 67092175 67131227 XM_017001276.1 0 - 67093004 67127240 0 9 1429,187,70,145,68,113,158,92,86, 0,3059,4076,11062,19401,23176,33576,34990,38966,
+
+The collections of stuff I downloaded from UCSC didn't include one of these, but
+the RSeQC site has one available for download. Actually, it has several BED
+files. I'm not sure which one is correct. I downloaded `hg38_RefSeq.bed`
+because it sounds the most like the GTF I used (`hg38.ncbiRefSeq.gtf`). Was
+that correct? Who knows?
+
+Now that I have that, I'm doing an initial run with:
+
+ tin.py --input data/05-alignment/clean/C0/C0.bam -r data/00-raw/hg38_RefSeq.bed
+
+It seems like it's going to take a long time. Guess I'll wait.
+
+The goddamn thing didn't output an ending timestamp. Come *on*. It took
+somewhere between 2-5 hours, but I have no idea how long because I wasn't
+watching it when it finished. I guess I'll do another run with a `time` prefix.
+Sigh.