User: DNAngel
DNAngel • 80
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Posts by DNAngel
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... Sorry for my ignorance but this would be different from a proportions test right? (Z-test)? ...
written 1 hour ago by
DNAngel • 80
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... Hi all,
Quick concept question here...
If I have two groups ("Functional" with 100 genes, "Control" with 50 genes) and I ran a bunch of models on each gene individually and found that "Functional" out of 100 genes, 50 were significant for a test, and "Control" (although I expected none) I got 10 s ...
written 2 hours ago by
DNAngel • 80
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... Hello all,
Just wondering - after assembling my reads to a reference protein-coding sequence for a bunch of genes, I happened to notice that for a couple certain clades I just did not get any sequence from them.
Is this a case of a gene being lost in the clade, or are their particular sequences too ...
written 17 hours ago by
DNAngel • 80
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... Hi all,
I posted my question in the PAML discussion group twice and haven't heard anything for months so hoping someone here can explain this to me:
I have a gene dataset with two partitions A and B, I separate the dataset into just A and just B to use for random-sites models to see if there's any ...
written 2 days ago by
DNAngel • 80
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... Hello all, I am trying to make sense of some unusual results I obtained for my dataset. I am testing for positive selection in several genes for my species between two clades that come from two different habitats (sunny and shady). Since sunny species diverged after and evolved from shady species, I ...
written 27 days ago by
DNAngel • 80
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... I saw that one. My bad. ...
written 9 months ago by
DNAngel • 80
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... Hi all,
I've written a large bash script for single-end paired reads which uses bwa mem. It works great. But now I have a new dataset that is paired-end and the only part I need to change is the beginning where bwa mem uses a reference file and sample files to align them. I cannot figure out how to ...
written 9 months ago by
DNAngel • 80
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... How would you modify this if you have many reference files to process for many fastq files?
If my reference.fasta files are saved in a large list in reflist.txt, and I have another directory with my fastq files to process how does one instead use parallel to process many reference.fasta files simul ...
written 12 months ago by
DNAngel • 80
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... I know but because I have multiple fastq ffiles to process for 1000s of ref genes (which the link you provided and others I've found here do not have this problem) I am unsure which part of my script to change. Do I use parallel to call the individual REF files of which I have thousands and in that ...
written 12 months ago by
DNAngel • 80
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... I've seen some posts here that have tried to parallelize bwa-mem for their sample data but all examples were paired-end data and the code was standalone (i.e. they only needed it for bwa mem and maybe converting SAM to BAM). But I also have to run my script for 1000s of different reference files and ...
written 12 months ago by
DNAngel • 80
• updated
12 months ago by
Pierre Lindenbaum ♦ 131k
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