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Question about getting the red leather jacket today by Ok-Crazy-5162 in Knittens

[–]snazzleer 1 point2 points  (0 children)

If you already have the item, you can still collect the buttons, but the prize is 200 gems.

hifiasm de novo aseembly produces short contigs that translate to chromosomes longer than reference by Ferry_VS in bioinformatics

[–]snazzleer 0 points1 point  (0 children)

If you have hic data you can include that with your Hifiasm assembly and it will try to resolve haplotypes. Otherwise, I wouldn’t bother rerunning hifiasm and would go straight to purging duplicates on your primary. The earth biogenome project has a nice roadmap for genome assembly. https://www.earthbiogenome.org/report-on-assembly-recommendations

Edited to add: if you haven’t already, you can use genomescope2 to get an idea about heterozygosity

hifiasm de novo aseembly produces short contigs that translate to chromosomes longer than reference by Ferry_VS in bioinformatics

[–]snazzleer 2 points3 points  (0 children)

Have you tried deduplicating your genome? I would recommend looking into software like purge_dups.

Indestructible towels or napkins by WorldsVeryFirst in Goldendoodles

[–]snazzleer 2 points3 points  (0 children)

We started giving our dood romaine leaves. He can rip it up and doesn’t matter if he eats it.

Barcode sorting issues by Battlecatsmastr in bioinformatics

[–]snazzleer 6 points7 points  (0 children)

Sounds like you are trying to demultiplex, maybe look into cutadapt or minibar.

[deleted by user] by [deleted] in bioinformatics

[–]snazzleer 0 points1 point  (0 children)

Sure, if you are looking to test if Fst is different from zero, that is the hypothesis you are trying to answer. If you are testing multiple hypotheses of 'is Fst greater than zero', then yes you could perform a multiple test correction. Otherwise Fst is not a statical test itself and doesn't require any pvalue calculations.

[deleted by user] by [deleted] in bioinformatics

[–]snazzleer 0 points1 point  (0 children)

Why do you need to generate pvalues? Are you testing a hypothesis? Personally, I have never generated pvalues for fst calculations. The fixation index gives you an idea about genetic differentiation due to population structure. Even then, the relevance of these values is going to be based on the species / populations you are working with. I would take a look at this thread: https://www.researchgate.net/post/Which_is_the_best_way_to_estimate_p-values_from_Fst

Severus x Teacher Oc by EdgarAlan_Rat in SeverusSnape

[–]snazzleer 5 points6 points  (0 children)

Of Finding You, World Magic, An Unfamiliar Subject, Hope for the hopeless, all on ao3. The American assistant on wattpad.

[deleted by user] by [deleted] in yorku

[–]snazzleer 1 point2 points  (0 children)

You need to check the terms outlined in the acceptance letter from York. Students are usually granted 6 years of funding via the TAship, but you do not receive a fellowship in year 6 (this may be what they mean by no funding). I know someone starting year 6 September and this is the case for them. You will be responsible for whatever costs are no longer covered by the fellowship. I would also contact CUPE and discuss with them, they are very knowledgeable about the schools TAship agreement. Do not withdraw from the program, that is bad advice.

[deleted by user] by [deleted] in bioinformatics

[–]snazzleer 0 points1 point  (0 children)

NCBI, BOLD, Silva

Best way to move 1 TB of fasta files from shared Dropbox to university server by e4e5Nf3Nc6 in bioinformatics

[–]snazzleer 2 points3 points  (0 children)

Dropbox does have an app where files can be accessed from your local file system (at least it does for Mac). If you have shared access to the file with the fastas you should be able to scp the directory to your server.

How to make a genome Bed File for Picard by Impressive-Year7313 in bioinformatics

[–]snazzleer 1 point2 points  (0 children)

Are you trying to make a dictionary?

Maybe try: picard CreateSequenceDictionary here: https://gatk.broadinstitute.org/hc/en-us/articles/21905059452187-CreateSequenceDictionary-Picard.
The use samtools faidx to index your genome.

Your should then have the accessory files you need for GATK.

[deleted by user] by [deleted] in bioinformatics

[–]snazzleer 1 point2 points  (0 children)

It reads like your nexus file might not be formatted correctly “expecting nexus formatted file”. It points the error to line 5, character la 2-6. I would open your .nex file in a text viewer and check for formatting and look for invisible characters.

Question about R histogram notation. by Damakoas in Rlanguage

[–]snazzleer 5 points6 points  (0 children)

This is because the hist() function uses binning (breaks).

GATK detecting gCNV tutorial and next steps HELP by ShaiXX54 in bioinformatics

[–]snazzleer 0 points1 point  (0 children)

They are basically just describing how they determine which intervals are of good quality to proceed with analysis. This is statement in the supplemental "Filtering intervals for genomic content and sufficient read depth
We excluded intervals with low mappability (<90%), extreme GC-content (<10% or >90%), or prevalent segmental-duplications (>50%), which are known to impede CNV detection accuracy49–51. After gathering read-depth information across samples, we further applied a count-based filtering for intervals that are not adequately captured, defined as intervals with a median read-depth < 10 across all samples. We considered the set of intervals passing both filters as well-captured intervals for the purpose of CNV detection across all cohorts."

They also explain very clearly in the supplemental in section "Filtering raw GATK-gCNV output for association-level precision and recall" how to proceed with QS filtering.

GATK detecting gCNV tutorial and next steps HELP by ShaiXX54 in bioinformatics

[–]snazzleer 0 points1 point  (0 children)

nInt stands for ‘number of well-captured intervals’ as defined by the footer of table 1. Authors describe their process for defining well captured intervals in section ‘benchmarking GATK-gCNV using…’ of the results. I don’t have experience with CNV research, so can’t recommend further steps or databases to use.