Playing with matches and CIGARs
Aligned reads in a SAM or BAM file typically have a Compact Idiosyncratic Gapped Alignment Report (CIGAR) string that expresses how the read is mapped to the reference genome.
When I first read the CIGAR operator table (above), I was confused by two things:
- the match,
M, operator description, “alignment match (can be a sequence match or mismatch)“, struck me as odd.
- the relationship between the
Xoperators isn’t explained in the spec.
I hope this blog post helps others with the same questions.[Read More]
Chabot 50K Trail Run Race Report
Late 2009 iMac HDD Replacement
The harddrive in my iMac (Late 2009 27”) died last weekend and I decided to replace it myself. Here’s some quick tips if you find yourself in the same situation. Not sure if disk errors are your problem? Boot you Mac and press “Command-V” during startup for verbose boot output. You’ll see messages about “Disk I/O Error” during boot.
There’s a great tutorial on iFixit that explains step-by-step how to replace the drive. I found my iMac had a 3.5” Hitachi Model HDE721010SLA330 SATA 3.0 Gb/s drive once I cracked it open. You can replace the drive with any 3.5” SATA drive you like. I chose to replace it with a comparable Western Digital drive that had more cache.[Read More]
From zero to Impala in minutes
This post is now hosted directly on the Cloudera blog. Cloudera will be able to provide much better support and more timely answers to your questions than I can.