User: thackl

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thackl2.8k
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Posts by thackl

<prev • 238 results • page 1 of 24 • next >
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Comment: C: Add metadata based on tree structure
... This is now actually implemented in ggtree https://yulab-smu.github.io/treedata-book/chapter7.html#composite_plots and https://yulab-smu.github.io/treedata-book/chapter10.html#scale-utilities ...
written 3 months ago by thackl2.8k
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Answer: A: R ggtree adding metadata based on tree structure
... If you are interested in some flexibility beyond ggtree's nice built-in functions, check out my blog post about an alternative approach: https://thackl.github.io/ggtree-composite-plots ...
written 3 months ago by thackl2.8k
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Comment: C: How to generate contigs from bam alignment
... They should look like in the reads, not like in the reference. ...
written 4 months ago by thackl2.8k
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Comment: C: How to generate contigs from bam alignment
... You can use `PREFIX=/path/to/where/you/want/proovread/to/be/installed make install` if you want to move proovread to a certain location. You don't need to do that, though. It will also just run without `make install` from the directory you downloaded it to. ...
written 4 months ago by thackl2.8k
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Comment: C: extracting one gene rpkm from 200 txt files
... You might want to add a `-w` to make sure not to get matches to other gene names containing your search pattern. Something like gene "ABC" might otherwise also match gene "ABCD" or gene "AABC2".. ...
written 5 months ago by thackl2.8k
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Comment: C: Get BUSCO gene descriptions
... Yeah, I was hoping you had moved on by now ;) ...
written 6 months ago by thackl2.8k
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Answer: A: Get BUSCO gene descriptions
... Just came across the same issue, and came up with a solution. Most BUSCO data sets are generated from OrthoDB. You can query OrthoDB via its API to map BUSCO IDs and pull the information. I've posted a short R snippet to automate this and produce a nice table https://thackl.github.io/BUSCO-gene-desc ...
written 6 months ago by thackl2.8k
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Comment: C: retrieve multiple bacterial genes and flanking regions
... OK, this worked for me on a dummy example. Minor fixes to old code & strip the flank annotations from IDs. Only problem, the final file doesn't contain "gene names" but id as chr:start-end... seqkit subseq --up-stream 200 --down-stream 200 --gtf genome.gff genome.fna > all-orfs-with-flanks.ff ...
written 8 months ago by thackl2.8k
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Comment: C: retrieve multiple bacterial genes and flanking regions
... Hmm, you're right. seqkit uses coordinates for ids instead of the gene_id from the gff... Hadn't thought about that. I don't have an easy fix for that atm. Need to think about it ...
written 8 months ago by thackl2.8k
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Comment: C: retrieve multiple bacterial genes and flanking regions
... Yes, something like the snippet below could work. Needs one little extra piece of command line magic, though. I'm assuming you are working on a bash-like command line: # get orfs with flanks as before seqkit subseq --up-stream 200 --downstream 200 --gtf genome.gff genome.fa > all-orfs-with-flank ...
written 8 months ago by thackl2.8k

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Commentator 9 weeks ago, created a comment with at least 3 up-votes. For C: bwa mem runs slowly the first time
Voter 6 months ago, voted more than 100 times.
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Which peak is homozygous and heterozygous in Kmer plot for Genome estimation
Scholar 8 months ago, created an answer that has been accepted. For A: Which peak is homozygous and heterozygous in Kmer plot for Genome estimation
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Which peak is homozygous and heterozygous in Kmer plot for Genome estimation
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: Which peak is homozygous and heterozygous in Kmer plot for Genome estimation
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