User: victoria_aleks
victoria_aleks • 30
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Posts by victoria_aleks
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... Dear all,
my RAXML run was interrupted after all bootstraps were completed. The RAXML specialists advice:
"However, since you already have the bootstraps, you can now
independently compute a couple of ML trees (see manual) and then use
these results to do post-analyses ..." (https://groups.google ...
written 19 days ago by
victoria_aleks • 30
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C: User-defined tree in MrBayes
... it finally worked when I wrote 'startvals tau = mytree' in one line :) thank you again! ...
written 8 weeks ago by
victoria_aleks • 30
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C: User-defined tree in MrBayes
... thanks, good idea. I spent already quite some time on all these small things...:)
if i may ask: do you use MB often? My dataset is quite big (180 protein seq., ~100000 amino acids), and I have read that Mr Bayes is not good for big datasets... ...
written 8 weeks ago by
victoria_aleks • 30
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C: User-defined tree in MrBayes
... thank you! but then it says:
"Could not find taxon 'Prot_ID' in list of taxa". what would that mean?
also, when I type:
...
startvals
tau = mytree
-- it doesnt find the command 'tau', neither 'topology'
when I type:
...
startvals tau = mytree
--it doesnt know what is 'mytree'
:(
...
written 8 weeks ago by
victoria_aleks • 30
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... Dear all,
I have a primitive question, I am afraid. I want to run MrBayes on amino acid sequences with the predefined tree, as random trees run does not reach conversion. Nevertheless, I can not find the command on how to do it. All the manuals and tutorials I have found say "User-defined trees can ...
written 8 weeks ago by
victoria_aleks • 30
• updated
8 weeks ago by
h.mon ♦ 15k
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C: extracting depth info from vcf
... ok, at the end we had to write our own script:) ...
written 6 months ago by
victoria_aleks • 30
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... hi Abdul, did you solve the problem?:) ...
written 6 months ago by
victoria_aleks • 30
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C: extracting depth info from vcf
... but also: can I extract exactly AD values, not only DP?? I want to know how many reads contain ref and how many contain alt nucleotides. ...
written 6 months ago by
victoria_aleks • 30
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Comment:
C: extracting depth info from vcf
... thank you a lot:) it all finally seem to work now! ...
written 6 months ago by
victoria_aleks • 30
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C: extracting depth info from vcf
... now it worked:) as I understand the script summated AD for ref and alt and wrote it into DP parameter. but now i try to use vcftools to extract this DP (for example, --depth or --geno-depth) and it reports on 'missing entries'. and i still cannot use gatk, i think, as i have only vcf files, no fasta ...
written 7 months ago by
victoria_aleks • 30
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