2022 Functional Genomics Lab Notebook


2022-01 January

2022-01-21 Friday

[2022-01-21 Fri 11:39] Setting up new server

So some issues. There's no power cable for the ssd. And I don't have internet access on the server yet. There's also no deb for megacli to download so I had to use alien to create it. But alien isn't packaged up for nixos, so I had to make a docker image and run alien in there, then put that on a usb and then move it to the server.

Basic overview: https://gist.github.com/fxkraus/595ab82e07cd6f8e057d31bc0bc5e779

Thought I was going to have to order a power cable for the loose ssd, but I found one on the power supply.

2022-02 February

2022-02-19 Saturday Goals and Planning


TODO Previous 5 years

Research Goals

TODO Next 3 years

Professional & Personal Goals

Next 3 years

2022-02-21 Monday

[2022-02-21 Mon 13:15] Goals and Planning Meeting

Three parts to my project
Random thoughts
Applied Genomics

2022-02-26 Saturday

[2022-02-26 Sat 20:38] Setting up raid controller and Julia

Issue with not being able to use megacli, was that I wasn't running it with sudo

sudo ln -s /opt/MegaRAID/MegaCli/MegaCli64 /usr/local/bin/megacli
sudo megacli PDList -aALL

To use the drives connected to the 2108/2208 controller, a RAID must be created. If using drives like in JBOD, each single drive must be created as a RAID 0 individually

Once again confirmed, going to need to make each disk a RAID 0

Installed storcli
wget https://downloadmirror.intel.com/685225/StorCLI_007.1704.0000.0000.zip
unzip StorCLI_007.1704.0000.0000.zip
sudo dpkg -i StorCLI_007.1704.0000.0000/Ubuntu/storcli_007.1704.0000.0000_all.deb
sudo ln -s /opt/MegaRAID/storcli/storcli64 /usr/local/sbin/storcli
Used storcli to setup disks

MegaRAID StorCLI — ASERGO Knowledge Base

# sudo -i
storcli /c0 set jbod=on
# Controller does not support JBOD
# :(

storcli /call/dall show all

storcli /c0 add vd r0 drives=245:0

for i in {4..12}; do
    storcli /c0 add vd r0 drives=245:$i

storcli /call/vall show

ZFS pool creation
sudo zpool create tank mirror /dev/sdd /dev/sde

Not sure if they should be Cache devices or SLOGs?

Porque no los dos?

Going to have a mirrored SLOG(To prevent data lose) and just throw both of them at the L2ARC cache, since it's just for reference and not for actual data. Might use them as a second SLOG

sudo zpool add -f tank log mirror /dev/sdj /dev/sdk
sudo zpool add -f tank cache /dev/sdl /dev/sdm
Made a scratch pool
sudo zfs create tank/scratch
sudo zfs set mountpoint=/scratch tank/scratch
sudo chown -R emiller:users /scratch/

2022-03 March

2022-03-07 Monday

[2022-03-07 Mon 10:00] Figure out nature of Transcripts   meeting

With Tae Hoon Kim

What the workflow will look like

Interesting eRNAs will be:

Useful LSI MegaCli64 Commands – Help Center

2022-03-20 Sunday

[2022-03-20 Sun 21:55] Ran groseq transcripts against TREs

There's a ton of reads still. Basically, there were still reads, so yay!

2022-04 April

2022-04-04 Monday

[2022-04-04 Mon 11:17] Meeting with Tae


2022-04-10 Sunday

[2022-04-10 Sun 22:12] Funnel Plot

import plotly.express as px
import pandas as pd

stages = [
    "All unannotated transcripts",
    "Transcripts that overlap with H3K4me1 and H3K27ac histone modifications",
    "Transcripts that satisfy cutoff for amplitude index and continuity index",
df_mtl = pd.DataFrame(dict(number=[127249, 21966, 10695], stage=stages))
df_mtl["Cell"] = "GM"
df_toronto = pd.DataFrame(dict(number=[88540, 34543, 14775], stage=stages))
df_toronto["Cell"] = "IMR"
df = pd.concat([df_mtl, df_toronto], axis=0)
fig = px.funnel(df, x="number", y="stage", color="Cell")

2022-04-18 Monday

[2022-04-18 Mon 10:00] Meeting with Tae

Feedback on Current Research Presentations
Applied Genomics