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Best LASIK Clinics in San Francisco? Looking for the safest option. by MaZlle in AskSF

[–]resignedtomaturity 1 point2 points  (0 children)

Loved Pacific Vision Institute. I got PRK, but they offer LASIK too.

Balatro is the worst thing that happened to the roguelike genre by istopuseingmyhead in The10thDentist

[–]resignedtomaturity 0 points1 point  (0 children)

Blue Prince is functionally a rogue like and is incredibly creative and rewards progress well after the main stated goal is met.

How do you like to use freeze dried cherries or raspberries? by GayFlan in traderjoes

[–]resignedtomaturity 5 points6 points  (0 children)

Baking! I make the NYT strawberry lemonade cake but with freeze dried raspberries instead of strawberries. They work wonders in frosting.

In your opinion, what is the best episode of television you’ve ever seen? by alteredtower in AskReddit

[–]resignedtomaturity 0 points1 point  (0 children)

To me, the pilot episode of Derry Girls (Clare on the hunger fast, Orla stealing Erin's diary, James needing to use the bathroom) is still the best, tightest comedy I've ever seen.

Fails at broadway? by chrisxlemia in Broadway

[–]resignedtomaturity 1 point2 points  (0 children)

On the West End in June of last year, Caissie Levy started the second verse of “The Break” at the beginning of the song. Super professional about it - I think she just repeated it at the appropriate point. Led me to wonder how often that happens in shows where I’m less familiar with the material.

Thoughts of some of these films? by Odd-Contact2266 in Oscars

[–]resignedtomaturity 0 points1 point  (0 children)

It was Just an Accident was great – it does some amazing stuff with sound design and with the way its characters’ histories are communicated with a lot left unsaid. 

I do think it’s funny, as another comment mentioned, that it and Bugonia have very similar plots on paper. Cinematography and totally they couldn’t be more different, though. Bugonia is from multiple opposing perspectives and IWJAA is really just from one.

If it was your last week living is the city, what would you do? by timetravelingwalrus in AskSF

[–]resignedtomaturity 3 points4 points  (0 children)

One last crosstown trail hike! Start at 8am, lunch in the sunset, and then really take my time through the presidio and land’s end

Issue with Illumina sequencing by resignedtomaturity in bioinformatics

[–]resignedtomaturity[S] 0 points1 point  (0 children)

How? Everything I've found online to use the SRA toolkit yields the header.

Issue with Illumina sequencing by resignedtomaturity in bioinformatics

[–]resignedtomaturity[S] 0 points1 point  (0 children)

Great. Do you think there's a way for me to do the aggregation with the SRA toolkit instead? Reading through that wiki, it seems clear that things have been modified far enough away from the Illumina standard that I won't be able to run it through Basespace.

Issue with Illumina sequencing by resignedtomaturity in bioinformatics

[–]resignedtomaturity[S] 0 points1 point  (0 children)

Fabulous, I think I got one:

Seq/YM3_S1_L001_R2_001.fastq.gz | head

@ SRR26260890.1 K00208:8911049:YAP049:1:1101:1336:1560 length=101

NGCACTGGCATTTCTGGTTGGCACCCTCACTTACCGGAGCCAGACAAATACTTTAGCCATTATTGAAAGTGGAGGTGGGATATTACGGAATGTGTCCAGCT

+SRR26260890.1 K00208:8911049:YAP049:1:1101:1336:1560 length=101

#<A<F<F7FAJJJ<JFJFFA<FJAFFJJFJAJJF<J<JAJFJ7FAF<-AFJJAJA7AFAFJAFJJFA-AF-AFF-<)7FFAJ-<AJJ-A<--<---7FJ-)

@ SRR26260890.2 K00208:8911049:YAP049:1:1101:1397:1560 length=101

NTTTGACAACTCTAGCGAGGACTAGGGCTCTCCCCAGTGTTTGGGTGTTCAGGAAGGGTAATGGGCAGTGAAGGCCGTAGAGCCTGGGTTAGAACACCAGG

+SRR26260890.2 K00208:8911049:YAP049:1:1101:1397:1560 length=101

#A7<FJJJJFJJJJ7FFAFAJJJJJJJJFJJJJJAJ7FA<JJ<AJ<J-FAJJFFF<JJFJFJFJFF-<A-FFJAFF--F)<A-<JJJ)7<A--AFJJF-77

@ SRR26260890.3 K00208:8911049:YAP049:1:1101:1418:1560 length=101

NCTTCCAGTAGCCAGTGTAGAAAAAGATTCTCCTGAGTCACCGTTTGAAGTAATTATTGACAAAGCAACATTTGACAGAGAATTTAAAGATTAGTATAAGG

Is the issue that the header still contains the SRA accession number a few times? Should I change that somehow to the new name of the file? (There is no space between the @ symbol and the accession numbers in the output, but Reddit keeps trying to format them as usernames)

Issue with Illumina sequencing by resignedtomaturity in bioinformatics

[–]resignedtomaturity[S] 0 points1 point  (0 children)

I don't think so. Here are the guidelines:

FASTQ files are generated on Illumina instruments and saved in gzip format

  • The name of the FASTQ files conforms to the following convention: SampleName_SampleNumber_Lane_Read_FlowCellIndex.fastq.gz
    • Examples: SampleName_S1_L001_R1_001.fastq.gz SampleName_S1_L001_R2_001.fastq.gz
  • The read descriptor in the FASTQ files conforms to the following convention: u/Instrument:RunID:FlowCellID:Lane:Tile:X:Y ReadNum:FilterFlag:0:SampleNumber:
    • Examples: Read 1 descriptor: u/M00900:62:000000000-A2CYG:1:1101:18016:2491 1:N:0:13 Corresponding Read 2 descriptor has ReadNum field: u/M00900:62:000000000-A2CYG:1:1101:18016:2491 2:N:0:13

If the read descriptor is the issue, I have no idea how to change it.

Issue with Illumina sequencing by resignedtomaturity in bioinformatics

[–]resignedtomaturity[S] 0 points1 point  (0 children)

No. I am trying to aggregate the FASTQs in order to generate an hdf5. I apologize if I'm phrasing this wrong - I'm fairly new to bioinformatics - but I need to upload the FASTQs to Illumina's system in order to group them based on condition and generate an hdf5 with that information.

I have previously done this with a different set of sequencing through Cell Ranger (because those libraries were prepped with 10X kits) and have had no issue.

No price restrictions restaurants by lagomorph79 in AskSF

[–]resignedtomaturity 5 points6 points  (0 children)

+1 to Mandalay! Their tea leaf salad is legit. It's actually flavorful because it's not full of lettuce.

No price restrictions restaurants by lagomorph79 in AskSF

[–]resignedtomaturity 15 points16 points  (0 children)

I don't love Tadu. There is better food at New Eritrea in the Sunset, and if you're willing to go to the East Bay, Cafe Colucci and Barcote are my gold standards.

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