Gas station without pumps

2013 November 12

Long weekend, little accomplished

Filed under: Uncategorized — gasstationwithoutpumps @ 22:47
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I just had a 4-day weekend, in which I got little more accomplished than a usual 2-day weekend.

Much of Saturday was spent trying to use PacBio reads to improve a draft genome of  a V. cholerae strain that  I had built with 454 reads a couple of years ago.  There was no problem getting blasr to map the reads, and I could call variants with “samtools mpileup”, though that took 2 CPU days to complete.  Unfortunately, that did not tell me what I really needed to know, which was whether the orignal assembly was in the right order.  I found a couple of places where the PacBio read mapping indicated problems (either the reads all terminated their mapping at nearly the same point, or they suddenly switched from aligning very well to aligning poorly).  Unfortunately, I’ve not yet figured out a good way to automate this detection, so I’m not sure I can find all the places which might have problems.  Dips in average quality of the mpileup consensus over 50- or 100-base windows pulls out the places where the alignments get bad, but not where they suddenly stop.  Furthermore, once I’ve identified the bad regions, I still need to break the genome apart there, rebuild the bad regions from the PacBio reads that map nearby, and see if I can stitch the genome back together (probably with extra repeats that had not been resolved in the 454 assembly).  I’m considering backing off and building a new genome assembly from just the PacBio reads (after cleaning them up using PacBio2CA and the 454 reads) and the Celera Assembler.  I can then compare the genome built from the PacBio reads and the one built from the 454 reads and resolve any discrepancies. Sigh, this project keeps getting bigger, just as I think I’m almost done.

On Sunday, I did a bunch of small tasks: raked leaves and shredded them, updated the grad alumni web page, announced the Freshman Design Seminar class (which will happen winter quarter, though once again as a “Group Tutorial” to prototype the course before submitting the official paperwork), wrote a letter of recommendation for a student applying to grad schools, scanned in the flyer for “Planet of the Abes” (the recent Dinosaur Prom show), scanned 35-year-old t-shirt of mine so that I can get another copy made, updated my paper list to include the just released PNAS paper, wrote a blog post, and caught up with a lot of my e-mail (though there are still some advising e-mails that I haven’t taken care of).

The flyer,  drawn by Hunter Wallraff, for the Dinosaur Prom Improv show.  Because the edge of the drawing was not reproduced on the flyer, I had to try to add it in by hand to get something usable for the titling of the video.  I did not correct the error in the URL for

The flyer, drawn by Hunter Wallraff who holds the copyright, for the Dinosaur Prom Improv show. Because the edge of the drawing was not reproduced on the flyer, I had to try to finish the S and add an E  in by hand for “Broadway Playhouse” to get something usable for the titling of the video. I did not correct the error in the URL for

On Monday, I did a lot of grading, wrote another blog post, used the Planet of the Abes flyer to make titles for the Dinosaur Prom video, and rendered the video (tying up my laptop all night).  I also cleaned up the scan of the old t-shirt and converted it to SVG so that a new silk screen printing can be done. I’ve tried looking for the copyright holder for the design, but I have no idea how to find him (or her)—Google image searches bring up nothing similar, and there is no signature on the design or the shirt. I started working on my slides for the talk I have to give on Thursday, but did not get much done.

This morning, I responded to more e-mail, wrote another blog post, did more grading, and returned the activity monitor I’ve been wearing for the past 2 weeks to the Sleep Center. In the afternoon, I did more grading at Gayle’s Bakery in Capitola, met with my son’s consultant teacher for a couple of hours, bought the usual weekly load of soy milk (only 2.5 gallons this week), did some other grocery shopping, finished the grading, recorded the grades, cleared the rest of the advising e-mail, and compared results on group theory problems with my son.  We’re a bit behind schedule there—he’s not finished all the Chapter 1 and Chapter 2 problems I assigned, and we’re supposed to be finishing Chapter 3 this week—I’ve not even assigned Chapter 3 problems yet.

Things I wanted to do this weekend but didn’t:

  • Get the slides done for Thursday’s talk
  • Get the Program Learning Objectives written for bioinformatics
  • Get assessment plans defined and written for the Program Learning Objectives for both bioengineering and bioinformatics.
  • Create a draft of a revised curriculum for the third track in bioengineering (which also needs a new name and a clearer focus).
  • Rewrite the handout for the next programming assignment in the Bioinformatics: Models and Algorithms courss.
  • Write code for looking for regions of the Helicobacter pylori genome that are possibly swapped in the current assembly and test for which rearrangement is most consistent with our data.
  • Start testing the BitScope differential input device they sent me.
  • Start working on Chapter 3 problems in group theory.
  • Start writing a paper on the segmenter that I described in my blog 3 months ago.
  • Clear the leaves off the roof before the rains start, since the leaves form dams that keep the rain from running off into the gutters properly.

There were probably other things, but I forget what they were now.  Once the to-do list gets longer than my piece of paper can hold, things fall off it.



  1. With regard to your PacBio issues: the latest software from the company (‘smrtanalysis’) includes bridgemapper (in beta). This pipeline maps raw pacbio reads to a reference (e.g., an assembly) and both lists and visualises split read mappings. This allows for finding regions with a high density of reads with a split mapping to the same position elsewhere, indicating potential assembly errors – or structural variations when comparing genomes. If you have a lot of PacBio coverage (preferably at least 100x), then a de novo, pacbio only assembly can yield a finished genome.

    Comment by lexnederbragt — 2013 November 13 @ 03:02 | Reply

    • I have about 200x, but I think the data is from an older run with earlier chemistry, so the read lengths are not what the newer PacBio runs that have been used for de novo assembly get. I’m going to try a de novo assembly, though. I also have only the fastq data for the reads not the original PacBio data (the data comes from a colleague of a colleague, and is all that is available). I’ll look into bridgemapper, though, and see whether it provides what I need.

      Comment by gasstationwithoutpumps — 2013 November 13 @ 08:13 | Reply

  2. My weekend was much more constructive. On Saturday I did laundry, cleaned the back yard, went through boxes of my Mother’s stuff (she passed this summer and all her possessions are still in our rec room), and went for a 5 mile hill run. Sunday I recovered from the 5 mile hill run, went to REI to see if there is anything I have to buy when their sale starts Friday (there is), bought Super Worms for the wife’s school lizard and continued to recover from the 5 mile hill run (which involves extensive couch time). I have learned with difficulty that running and mountain biking use very different muscles. In the summer I mountain bike almost exclusively, in the winter I run so I stay in half way decent shape for mountain biking. In the spring and fall I suffer. So in all my weekend was so much more constructive.

    Comment by Garth — 2013 November 13 @ 07:36 | Reply

    • My only significant exercise is utility bicycling (commuting and shopping). I did very little of that Saturday through Monday, but Tuesday I had about 11 miles of riding (mainly to the sleep center to drop off the activity monitory and sleep log, as Gayle’s Bakery, the school where I met with the consultant teacher, and grocery shopping were all more or less on the way home). The leaf raking on Sunday was some exercise—we had an enormous pile of leaves that we had raked together for Halloween, and I had to get that off the lawn and onto the driveway, where I shredded it with my electric mower.

      Comment by gasstationwithoutpumps — 2013 November 13 @ 08:17 | Reply

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