--- a/README.markdown Thu Mar 19 15:58:56 2020 -0400
+++ b/README.markdown Thu Mar 19 20:32:36 2020 -0400
@@ -1175,3 +1175,54 @@
Checked in on the STAR progress. It's actually only taking ~5-10 minutes to run
each alignment. That's not nearly as bad as I expected.
+
+Initial alignments finished. Started digging into what I can actually *do* with
+the results. I found the Integrative Genomics Viewer (IGV) that seems
+promising. Downloaded it and loaded the genome into it, then tried to load the
+alignments but apparently it wants BAMs, not SAMs, and additionally it wants
+indexes of the BAMs.
+
+I looked into how to convert the SAMs to BAMs+indexes. Went down a bit of an
+unnecessary rabbit hole, but it was still productive. My initial attempt was
+using `samtools` to do a bunch of conversion:
+
+ STAR … # produces Aligned.out.sam
+
+ samtools view -S -b Aligned.out.sam > sample.unsorted.bam
+ samtools sort sample.unsorted.bam > sample.bam
+ samtools index sample.bam
+
+This worked, but took a while and wrote a bunch of intermediate files I don't
+really need. Eventually I realized that STAR can produce sorted BAM files
+itself, so all I need to do with `samtools` is the final indexing. Learned
+a bunch about running STAR too. One nice way to save time across all the
+alignments is to have STAR load the genome index into shared memory once at the
+beginning and use it for all the alignments, the flush it out at the end:
+
+ function cleanup {
+ STAR --genomeDir "${genome}" --genomeLoad Remove
+ }
+
+ trap cleanup EXIT
+
+ STAR --genomeDir "${genome}" --genomeLoad LoadAndExit
+
+Then the STAR invocations look like:
+
+ STAR \
+ --runMode alignReads \
+ --runThreadN $CORES \
+ --genomeDir "${genome}" \
+ --genomeLoad LoadAndKeep \
+ --limitBAMsortRAM "${sortram}" \
+ --outSAMtype BAM SortedByCoordinate \
+ --outBAMcompression 0 \
+ --outBAMsortingThreadN $CORES \
+ --outFileNamePrefix "${outdir}/" \
+ --readFilesIn "${in1}" "${in2}"
+
+I tried putting the temporary directory on `/dev/shm` but it ended up being too
+much with the persistent genome index also in RAM. Unfortunately my order from
+Crucial is still backordered. Oh well, I'll just watch more TNG while I wait
+for all the alignments to complete.
+