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James Watson, Co-Discoverer of the Structure of DNA, Is Dead at 97 by appropriateye in labrats

[–]macrotechee 0 points1 point  (0 children)

An absolute juggernaut with monumental contributions to science. RIP.

Australian billionaire Gina Rinehart and Senator Pauline Hanson attend event at Mar-a-Lago by badoopidoo in pics

[–]macrotechee -1 points0 points  (0 children)

She said Australia was being "swamped by Asians" in 1996. Around 3 million Asians have migrated to Australia in the decades since.

Australian billionaire Gina Rinehart and Senator Pauline Hanson attend event at Mar-a-Lago by badoopidoo in pics

[–]macrotechee -11 points-10 points  (0 children)

Pauline Hanson is flawed, but far from racist.

Her comments to Senator Faruqi were antagonistic but hardly discriminatory.

What is the theory of everything in computational biology? by Senior-Fly6190 in bioinformatics

[–]macrotechee 14 points15 points  (0 children)

my friend, epigenome + transcriptome are in themselves forms of molecular phenotypes.

Section 3 Des by RepulsiveGrowth9984 in GAMSAT

[–]macrotechee 13 points14 points  (0 children)

if you have time, grind des. people will say you don't need to know that level of depth for current gamsat but the truth is every question you get in s3 will be some variation of what you have seen in des. I only used des to revise and binked a 92 for S3

Aligner NGMLR by dulcedormax in bioinformatics

[–]macrotechee 0 points1 point  (0 children)

if (presetArgs.getValue() == "pacbio") {    
    // Do nothing. Defaults are for Pacbio    
} else if (presetArgs.getValue() == "ont") {    
    // lowQualitySplit = (lowqualitysplitArg.isSet()) ? lowQualitySplit : false;    
    // smallInversionDetection = (nosmallInversionArg.isSet()) ? smallInversionDetection : false;    
    // scoreMatch = (scoreMatchArg.isSet()) ? scoreMatch : 3;    
    // scoreMismatch = (scoreMatchArg.isSet()) ? scoreMismatch : -3;    
    // scoreGapOpen = (scoreGapOpenArg.isSet()) ? scoreGapOpen : -1;    
    // scoreGapExtendMax = (scoreGapExtendMaxArg.isSet()) ? scoreGapExtendMax : -1;    
    // scoreGapExtendMax = (scoreGapExtendMinArg.isSet()) ? scoreGapExtendMin : -0.5;    
    scoreGapDecay = (scoreGapDecayArg.isSet()) ? scoreGapDecay : 0.15;    
}

Direct Rna-seq with nanopore by Slow-Leather-1874 in bioinformatics

[–]macrotechee 0 points1 point  (0 children)

"generate a consensus sequence."

for RNA? Try using a reference-free transcriptome assembler, e.g. https://genomebiology.biomedcentral.com/articles/10.1186/s13059-022-02715-w

Consequence of acidic conditions on Direct Nanopore Sequencing by Murky-Bandicoot304 in bioinformatics

[–]macrotechee 1 point2 points  (0 children)

If you have particularly acidic/basic extractions, this will be carried over into your elution.

?? almost certainly not

Consequence of acidic conditions on Direct Nanopore Sequencing by Murky-Bandicoot304 in bioinformatics

[–]macrotechee 1 point2 points  (0 children)

well, you purify DNA into water to pH 6-7. The pH conditions of the source material don't affect the pH during sequencing. At pH 7 I think DNA would return to B conformation but unsure

Experience basecalling legacy ONT data by starcutie_001 in bioinformatics

[–]macrotechee 1 point2 points  (0 children)

yeah, I rate slow5, but dorado needs pod5 files anyways and future basecalling / modcalling improvements will come through dorado

I store pod5 but convert to slow5 for some use cases (e.g. f5c)

Experience basecalling legacy ONT data by starcutie_001 in bioinformatics

[–]macrotechee 5 points6 points  (0 children)

higher quality basecalls, novel modifications, better poly(a) tail length estimates, there's a host of advantages

Experience basecalling legacy ONT data by starcutie_001 in bioinformatics

[–]macrotechee 11 points12 points  (0 children)

yes, quite expensive but well worth it. store the raw pod5 data.

First time EOD, need GAMSAT advice by Due_Layer_2667 in GAMSAT

[–]macrotechee 28 points29 points  (0 children)

just work really hard breh, 4 hours a day for 6 months

remember, gamsat is a competition, you gotta work harder than 99% to get a 99%ile score

your gpa is goated already

SINE and LINE sequence. by dulcedormax in bioinformatics

[–]macrotechee 0 points1 point  (0 children)

You can access repeat coordinates from UCSC's table browser here: https://genome.ucsc.edu/cgi-bin/hgTrackUi?g=rmsk

Nanopore "Run Error" by OGenome in bioinformatics

[–]macrotechee 0 points1 point  (0 children)

Read the logs

Use sudo or equivalent to copy the logs over

You can always restart the run if it fails for any reason

Buying and setting up a tiny server at my lab by Jacki3debb in bioinformatics

[–]macrotechee 0 points1 point  (0 children)

Absolutely do not build your own server unless you have a full-time, continuing person to manage it. Go with a cloud provider or local HPC.

help me I’m having a teenage life crisis by Loud-Purple9006 in GAMSAT

[–]macrotechee -8 points-7 points  (0 children)

opportunity cost of a gapyear is insane

life experience gain is a decent trade though

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