# HG changeset patch # User Steve Losh # Date 1582606575 18000 # Node ID 0f1de4b551b0f2fc3bc4954f6ef58913ff041cf0 # Parent 0e18286c1a1a38b8447bf8f10e9a09dd80352bdb Update diff -r 0e18286c1a1a -r 0f1de4b551b0 README.markdown --- 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.