C. virginia methylation analysis:

Steven asked me to run the C. virginica BS-Seq data we had from an oil exposure trial through the Bismark. So far I’ve got the files copied over and error checked, but in the process crashed Unity enough such that it necessitates a reboot of Emu to restore functionality. I’ll do this after the blastx on Marcos’ strand specific data is finished and get back to work on Bismark.

Installing dammit on Emu:

Following the instructions from here made it all pretty straight forward. You heard that right, a bioinformatics program that installed properly and straight forward the first time. They do exist!

Lets give it a test run.

First, we check that all the dependencies we need are installed:

Screen Shot 2017-04-20 at 9.25.20 AM

That looks good.

Screen Shot 2017-04-20 at 9.27.53 AM

Thats not so good, so lets download and prep the databases we need.

after running dammit databases --install and waiting around, it looks like were ready to kick the tires with Marcos’ fasta file by executing dammit annotate ~/Documents/marcos_trinity/Trinity.fasta.

Then we wait for some output!

Yaamini’s Notebook: Manchester Day 62

Laura went out to Manchester today and graciously cleaned my oysters

She found one dead in bag Tank 3B. She shucked it open to check for anything unusual, but found nothing.



Figures 1-2. Dead oyster found in bag Tank 3B.

Table 1. Updated number of oysters in each bag per tank.

Tank A B Total
1 8 9 17
2 9 8 14
3 7 6 13
4 9 8 17
5 9 9 18
6 8 8 16
Total 50 49 98

There was also a lot of stringy stuff in the tanks, probably due the higher oyster density.



Figures 3-4. Stringy stuff found in my tanks.

Laura increased the flow on all tanks. She thinks the stuff may be related to the algae paste we feed the oysters. More information to follow.

from the responsible grad student http://ift.tt/2oU8NFI

Yaamini’s Notebook: Downloading Metaanalysis Data

It’s not as easy as clicking a button

To download selected runs from the SRA database, you have to use samtools. I documented my process in this Jupyter notebook.

In R, it’s easy to create a script to download SRA data with samtools. I modified my script from Sean’s.

 SRA.list <- c("SRR1693528", "SRR1693531", "SRR1693532", "SRR1693534", "SRR1693537", "SRR1693538", "SRR1696820", "SRR1696826", "SRR1696827", "SRR942533", "SRR1696867", "SRR1697248", "SRR1696868", "SRR1045858", "SRR3742302", "SRR3742311", "SRR3742313", "SRR3742315", "SRR3742316", "SRR3742317", "SRR3742318", "SRR3742319", "SRR3742320", "SRR3742321", "SRR3742322", "SRR3742323", "SRR3742324", "SRR3742325", "SRR3742326", "SRR3742327", "SRR3742344", "SRR3742345", "SRR3742346", "SRR3742347", "SRR3742348") #Make a list of all SRA run codes for data I want to download. I excluded run codes from data already downloaded by Sean and Grace. setwd("") #Set working directory to a folder where you can download data. My data is currently downloading on emu. for(i in 1:length(SRA.list)) #Create a for loop so each SRA run specified in "SRA.list" is downloaded as a .fastq file and zipped. { system(paste0("/Users/Shared/Apps/sratoolkit.2.8.2-1-mac64/bin/fastq-dump ", SRA.list[i])) system(paste0("tar czf ", SRA.list[i], ".fastq.tar.gz ", SRA.list[i], ".fastq")) system(paste0("rm ", SRA.list[i], ".fastq")) }  

Sean’s keeping tabs on my files as they download on emu. Once downloaded, he’s moving them to his scaphapoda directory. When they all download, I’ll move them to my directory in owl so I know where it is!

from the responsible grad student http://ift.tt/2pHrrn4

Unexpected Hyak login change:

Yesterday the UW Payroll people turned on the two-step authentication through an iPhone/Android app called Duo. I thought this just hooked in with my UNet ID for things like payroll and myuw related things, but apparently it extends to logging in to Hyak also.

When I logged in to Hyak this morning, I was greeted with this different password prompt.

Screen Shot 2017-04-20 at 8.26.16 AM

which popped up the Duo app on my phone, asking me to approve or deny a connection to hyak.uw.edu. I didn’t have to use the Entrust token one time key anymore, so maybe in the future we won’t have to request these for new users who are using the 2SA system through Duo?