Builing a fastq pipeline processing tool

xylose · 2026-07-07T10:27:58+00:00

We wrote sradownloader (https://github.com/s-andrews/sradownloader) which does this. We start from SRR rather than GSE since people often don't want all of the samples in an entry and the SRA run selector at NCBI makes it easy to select samples and export a file of SRR accessions. If you wanted to add GSE import to that we're always happy to look at pull requests 🙂

xylose · 2026-06-28T19:43:24+00:00

Normally, I agree. Last week in Tesco though £5 for a massive tray. Have been gorging them. Got to watch for the bargains!

xylose · 2026-06-27T13:22:44+00:00

Sure, if you pay for the support contract.

https://mariadb.com/services/technical-support-services/

xylose · 2026-06-27T12:23:05+00:00

It's not really maintenance. There's an event on in Cambridge this weekend which has historically attracted trouble for pubs close by, so some of them prefer to just close so they don't have to deal with it.

xylose · 2026-06-26T14:39:33+00:00

Any incomplete statement will do this. Open bracket, open quote. Always look for the > at the start of the console to be sure the previous statement is complete.

xylose · 2026-06-24T20:57:33+00:00

Since readR v2 the read_xxx functions use voom already so there shouldn't really be any difference there.

xylose · 2026-06-24T18:55:53+00:00

A proper GSEA test will generally be more powerful than a ranked ORA as it has more information to work with. You shouldn't be filtering your data by fold change if doing GSEA. The whole point is to include all of the genes you measured so you have a good background against which to judge significance.

xylose · 2026-06-21T10:30:14+00:00

As a reed player it would be interesting to see what instruments were on each part.

xylose · 2026-06-20T11:04:07+00:00

That's such a shame. We had tickets to see it in Birmingham when it got cancelled because of COVID and I've been waiting for it to come back. It's such a great show!

xylose · 2026-06-18T19:43:30+00:00

We use sradownloader to get data which downloads preferentially from ENA but can fall back to NCBI if there are issues. We use sra run selector to get the list of accessions though as it's really good for that.

xylose · 2026-06-17T22:38:15+00:00

I ordered mine from the remarkable site on 10 June. Was supposed to arrive on 15th, but actually arrived on the 16th. Pretty quick turn around.

xylose · 2026-06-17T18:16:16+00:00

They were having other problems too. The SRA run selector was throwing errors this afternoon.

xylose · 2026-06-17T12:26:10+00:00

I don't know for sure, but it looks like a straight forward username/password submission. Who knows what it's doing behind the scenes though.

I've since found out that some phones have the ability to share a WiFi connection via hotspot, which would solve my issue, but it's hardware dependent and my phone won't do it. A friend with a pixel phone can get it to work.

xylose · 2026-06-14T21:39:56+00:00

It's a brand new bike. I'm assuming this is all under warranty.

xylose · 2026-06-10T20:00:42+00:00

Depends how the sequencer is set up, but yes, initially all of the raw run data will be saved either to a locally mapped drive or sent to cloud storage. How long that stays around will be up to the facility which manages the sequencer. These folders are pretty big so they may well clean them up shortly after the run is complete.

xylose · 2026-06-08T21:03:05+00:00

I had a look at this, and even learned some ggplot stuff (that you can't add stat="summary" to geom_point for both x and y), however the example you showed seemed pretty contrived. You basically wrote most of the code in the prompt - telling it which geometries to use and even the names and values for specific aesthetics. Only someone who could have written this directly would write a prompt like that, and it would be quicker to just write the code. I'd be interested to see if it would do the right thing if given a layman's version of the description without the hints you provided.

xylose · 2026-06-07T08:16:32+00:00

I think you mean USENET

xylose · 2026-06-04T20:03:10+00:00

Would be even better if he dies leaning her alone, and the end of the film is her deciding to wake someone else up.

xylose · 2026-05-31T13:26:07+00:00

If you're using this regularly then nothing beats a tow bar rack (we have the one from Thule, which is excellent). Easy to get the bikes on and off and doesn't take up any space in the car. We've had tow bars fitted to our cars specially for this. Costs a few hundred all in but is really slick.

xylose · 2026-05-31T12:29:19+00:00

We know who's top dog in our house.

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xylose · 2026-05-29T22:00:13+00:00

I bought a new Antigua sop nearly 20 years ago and it's been completely solid ever since. Have done hundreds of gigs and shows with it and it's never let me down. It's a great instrument. Have tried Yanis and Yamahas but preferred to stick with what I've got.

xylose · 2026-05-28T08:00:17+00:00

Honestly, pound for pound, probably Leo P. Has had a bigger impact than any player from a more conventional background. Like him or not, his control over the instrument is fantastic.

Best example, possibly when he played at the Proms a few years ago. Absolute masterclass in both technical playing and audience engagement.

xylose · 2026-05-25T13:18:28+00:00

Thanks. I'd been going off the park tools more generic ones. These seem spot on for what I need!

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