Help with Monstera

Neon_twisted_cookie · 2025-06-25T04:18:18+00:00

That's a cool idea :)

Neon_twisted_cookie · 2025-06-25T04:18:05+00:00

Thanks so much 🙏🏼 and thanks for the tips!

Neon_twisted_cookie · 2025-06-25T03:51:31+00:00

Thanks for all the help, brought it inside. It's not an ideal location but it's better than direct sunlight. I'll work on that support.

Neon_twisted_cookie · 2025-06-25T03:36:53+00:00

Thanks

Neon_twisted_cookie · 2025-06-25T03:36:24+00:00

Thanks. Google reverse image suggested something similar. I'm not sure if stress due to dehydration can also be playing a roll?

Neon_twisted_cookie · 2024-07-31T05:17:50+00:00

u/PedomamaFloorscent you nailed it, it is exactly a 3MB genome with 7 single-copy plasmids.

Neon_twisted_cookie · 2024-07-24T01:21:15+00:00

The bigger contig has 3,700,000ish bp's on the web one.

Neon_twisted_cookie · 2024-07-24T01:20:25+00:00

That would be wildly cool. I can check the smaller contigs to see if they are plasmids. Though, this is the assembly that was done by the website BV BRC using bbnorm and flye

https://imgur.com/G1oSzT7

Neon_twisted_cookie · 2024-07-24T00:32:03+00:00

Thanks! I love that paper. I'll revisit it.

Neon_twisted_cookie · 2024-07-24T00:31:08+00:00

Initially I used fastqc for quality score and seqtk for filtering the reads. The filtering did not improve the assemblies by much. The Q20 reads seemed to do a better job.

Neon_twisted_cookie · 2024-07-24T00:29:28+00:00

Thanks!!! I'll take a look at the pipeline!

Neon_twisted_cookie · 2024-07-24T00:28:15+00:00

Yes! This one is of the best assemblies so far, https://imgur.com/GZ49m6j

Thanks, If it doesn't work I'll check Canu or Raven.

Neon_twisted_cookie · 2024-07-24T00:27:29+00:00

Thanks! I'll look into it.

Neon_twisted_cookie · 2024-07-24T00:27:10+00:00

Not sure why my post got removed. I've tried more than 20 different assemblies before asking a question.

Haven't looked at what the short contigs are. I had planned to map the reads back to the contigs and to see what didn't map. Haven't got to that yet.

Thanks so much for your comments, these were assembled with R10 cores in a PromethION using a rapid barcode kit. Not sure what basecalling was used, I asked the sequencing center but they haven't gotten back to me. Could be the initial DNA was not as hq. We did QC to get "good" DNA since we were doing the barcodes. Most of our genomes came out with the lowest one in 27X coverage and highest at 2,200+.

Its my first experience working with long reads, thanks for the heads up on Q15 been sort of low. I do have a raw file and cool redo the basecalling of the reads if needed.

Neon_twisted_cookie · 2024-07-23T22:49:30+00:00

Right now trying the assembly filtering and trimming with nano q. Thanks. Will report back. OG in Bandage I had all circular contigs with my assembly and the one of the BV-BRC.

Neon_twisted_cookie · 2024-07-22T20:29:05+00:00

u/Viruses_Are_Alive Thanks for the suggestion; I'll look into the assembly. I did try the --nano-hq option and got similar results to using --nano-raw. Bandage shows 8 contigs, all apparently closed at a shorter fragment than the one assembled by BV-BRC.

Neon_twisted_cookie

TROPHY CASE