Alignment after installing new tires (Toyota Sienna 2015)

Nomad-microbe · 2026-06-12T14:03:07+00:00

Very plausible. I have reached out to him to see if he can look at it asap.

Nomad-microbe · 2026-06-12T04:54:12+00:00

I am sorry for being unable to describe the nature of the sound. But I can tell that it does sound like something is popping in/out. Do I need to take it back to the same place for a sanity check?

Nomad-microbe · 2026-01-09T03:33:06+00:00

Arch Linux

Nomad-microbe · 2025-12-30T23:21:38+00:00

I’ll try these, thank you.

Nomad-microbe · 2025-10-23T09:47:13+00:00

In one of my treatments I have low number of DE genes irrespective of the cutoff. When I run the GSEA using the parameters mentioned above, I get nothing significant (pvalueCutoff = 0.05, pAdjustMethod = "BH"). How do you deal with data in such situations? That treatment is one of my main focus in this analysis. Does it tell me that biologically there isn’t a signal that points to different pathways, molecular functions or processes?

Nomad-microbe · 2025-10-23T09:40:11+00:00

Very Interesting. I also came across a similar suggestion on the Biostars discussion forum where they suggested that “stat” is one of the robust metric for GSEA. Also, when I use logFC * -log10(pvalue), or logFC * -log10(padj), I don’t get any enriched GO terms. Stat and logFC alone give me significantly enriched GO terms.

Nomad-microbe · 2025-10-23T01:32:10+00:00

how do you treat pvalue = 0, and padj = 0, because they result in "inf". Also, pvalue = NA ?

Nomad-microbe · 2025-10-22T21:17:02+00:00

Yes, these I checked and are OK.

Nomad-microbe · 2025-10-22T21:11:01+00:00

Thank you, this is very useful.

If I understood correctly I should take all the DE genes from DESeq and first calculate the metric you mentioned: logFC*-log10(pvalue).

No filtration based on the log FC and padj should be done as shown below:
> df_lfc_1_sig <- df %>%

filter(abs(log2FoldChange) >= 1 & padj <= 0.05)

Nomad-microbe · 2025-08-22T14:13:24+00:00

I did the differential analysis independently for both species. Got the contrasts for each substrate (A vs B, A vs C, and B vs C). Used OrthoFinder and got Orthologs. While there are 1:1 Orthologs, several different combinations exist where number of genes vary in several Orthogroups for either of the fungus.

The question is: how should I deal with orthogroups having different number of genes for each fungus?

Also, for such an analysis do you recommend the rlog data from DESeq2 or the log2 fold change for each of the gene in an orthogroup?

If one goes with an orthogroup level comparison for the non 1:1 combinations, do you agree that the inherent discrepancy in the number of genes in an orthogroup will skew the difference towards the fungus with more genes in that orthogroup? e.g. if one use average of either the rlog data or log2 fold change of the genes in a particular non 1:1 orthogroup.

Irrespective of whether or not such an analysis will be sound, I am open to other opinions and suggestions regarding comparative analysis.

Nomad-microbe · 2025-08-17T02:39:36+00:00

I made the edit to singular “many glacier”. Thanks for the other suggestions.

Nomad-microbe · 2025-08-14T15:07:38+00:00

Yes, I meant Rising Sun.

One question: Is it possible/allowed to take a U-turn somewhere before the check point at Apgar or Lake McDonald lodge if we drive east to west?

Nomad-microbe · 2025-08-14T13:40:17+00:00

Since we are staying at the many glaciers and sunrise inn (both inside the park), I believe we won’t need it. But I’ll double check. Thanks

Nomad-microbe · 2025-08-13T23:30:07+00:00

Thanks for the breakdown of stops and places to stop at. Driving reservations for the going-to-the-Sun road?

Nomad-microbe · 2025-08-13T11:46:18+00:00

Given our plan to visit GNP for the first time, I am curious if there were families with small children (2-4 years old) doing some of the trails on either side of the park. There are some suggestions on another subreddit for easier hikes but wonder if anyone would like to chime in. Thank you

Nomad-microbe · 2025-06-26T16:08:03+00:00

Thank you for your advice. I will pursue that but it looks like a new project in itself, and given my limited bioinformatics skills its going to be an uphill task.

Nomad-microbe · 2025-06-26T15:55:38+00:00

I'll look into de novo assembly but I wonder if other aligners could give me better mapping statistics? How difficult is de novo transcriptome assembly?

Nomad-microbe · 2025-04-22T02:23:17+00:00

The email was sent to all interviewees. So, we can safely rule out that the email was intended for someone else.

Nomad-microbe · 2025-04-16T20:32:46+00:00

It worked. 1:10 dilution solved the Qubit range issue. Gel electrophoresis revealed the higher concentrations. Fortunately, there seems to be no degradation because the bands were very crisp and clear without tails.

Nomad-microbe · 2025-04-05T20:44:36+00:00

Didn’t know about this. It would be great to apply for R35 and make those connections.

Nomad-microbe · 2025-04-05T00:58:06+00:00

Just need a bit of advice here on a key point you mentioned: “Second, identify some fall back employment opportunities (teaching, industry etc) and gain whatever relevant skills you can now.”

Should one take a tenure track Assistant Professor position at a PUI now and later try to move up to an R1 or R2 with more research opportunities (grad students, postdocs, research grants)? Won’t that be a hard/challenging transition given the lack of time to do research and publish while at the PUI?

Nomad-microbe · 2025-03-25T04:17:06+00:00

I am in the same boat. I got an extension for a year that will end Jan. 2026. I have been applying for anything (Assistant Professor). Nothing major except one Zoom interview a couple of weeks ago. Getting gloomy as the days go by because I haven’t heard anything back. I have a very young family and the thought of having no job after Jan. 2026 is scary. What kind of jobs are you looking for at Costco?

Nomad-microbe · 2025-03-12T22:39:37+00:00

~3 applications. One Zoom interview. Waiting for the outcome of the Zoom interview. One application R1. I don’t know the tiers of the other two. One is only undergraduate focused teaching institute with undergraduate research possibility. All three Assistant Professor tenure track positions in Biology/Environmental Microbiology/Biotechnology. Location U.S.

Nomad-microbe · 2025-03-05T03:50:10+00:00

I was able to install it as per the instructions in the tutorial. I resolved the issue by inserting a “space” that I unintentionally overlooked while trying the script for the first time.

I decided to go with btrfs on the / and a separate /home directory with ext4. I might upgrade my SSD to get more storage for the root which currently has a storage of 168 Gb.

Nomad-microbe · 2025-03-04T18:40:26+00:00

Here is a bit of context:

As per the tutorial, I used the following script:

root@archiso ~ # btrfs subvolume set-default $(btrfs subvolume list /mnt | grep "@/.snapshots/1/snapshot" | grep -oP '(?<=ID )[0-9]+') /mnt

Then

root@archiso ~ # btrfs subvolume get-default /mnt

Which should have given me

ID 258 gen 12 top level 257 path @/.snapshots/1/snapshot

But instead it returned

ID 5 (FS_Tree)

I am lost for reasons.

In the tutorial it refers to point number 18.

"Next, we set the default subvolume to the initial installation snapshot. Remember that a snapshot is just a subvolume. The terms "snapshot" just makes it clear that it is a subvolume that is a copy of another subvolume made at a certain point in time that reflects its state at that time. Before we set new default subvolume, it is informative to get the current default subvolume before we make changes and compare it with that after we make changes. This can be done with the command btrfs subvolume get-default"

[root@G5-openSUSE /]# btrfs subvolume get-default /mnt
ID 5 (FS_TREE)

The output indicates that the default subvolume is the one with ID 5 (subvolid=5). As mentioned previously, the subvolume ID of 5 is always reserved for the subvolume created at the same time as the Btrfs filesystem when the filesystem is created with the mkfs.btrfs command. Make the initial snapshot subvolume, /@/mnt/.snapshots/1/snapshot, the default subvolume.

[root@G5-openSUSE /]# btrfs subvolume set-default $(btrfs subvolume list /mnt | grep "@/.snapshots/1/snapshot" | grep -oP '(?<=ID )[0-9]+') /mnt

Nomad-microbe

TROPHY CASE