--- a/README.markdown Mon Feb 24 20:40:34 2020 -0500
+++ b/README.markdown Mon Feb 24 23:56:15 2020 -0500
@@ -1006,3 +1006,10 @@
genome but it complains that it requires the genome to be uncompressed. Tried
to trick it into working by psubbing `zcat` but that didn't work. Gave up and
decompressed the damn reference.
+
+Once the genome index was built, started aligning the reads. It failed right
+away complaining about a zero-length read. `zcat | grep`ing showed the read as
+being there in both files, *but* I bet this was an issue of the pairs getting
+out of sync because we grepped out the overrepresented sequences naively. Tried
+restarting the alignment on the original data and it's still going, so that's
+probably it. Need to figure out how to filter those bad reads properly tomorrow.