User: DNAngel

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DNAngel80
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Posts by DNAngel

<prev • 88 results • page 1 of 9 • next >
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Comment: C: Determining if the number of significant results between two categories is signi
... Sorry for my ignorance but this would be different from a proportions test right? (Z-test)? ...
written 1 hour ago by DNAngel80
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Determining if the number of significant results between two categories is significantly different?
... 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 ...
statistics written 2 hours ago by DNAngel80
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How to know if it is missing a gene or assembly error?
... 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 ...
bioinformatics bwa assembly written 17 hours ago by DNAngel80
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PAML sample size question and variation in results
... 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 ...
paml written 2 days ago by DNAngel80
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Understanding PAML results between random-sites and clade model C.
... 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 ...
paml written 27 days ago by DNAngel80
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Comment: C: How to loop over multiple files for BWA MEM in bash for loop?
... I saw that one. My bad. ...
written 9 months ago by DNAngel80
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(Closed) How to loop over multiple files for BWA MEM in bash for loop?
... 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 ...
bwa bash written 9 months ago by DNAngel80
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Comment: C: Optimize bwa mem in parallel on a SLURM cluster
... 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 DNAngel80
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Comment: C: How to parallelize bwa mem for single-end data within a larger bash script?
... 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 DNAngel80
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How to parallelize bwa mem for single-end data within a larger bash script?
... 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 ...
bwa-mem gnu-parallel bash written 12 months ago by DNAngel80 • updated 12 months ago by Pierre Lindenbaum131k

Latest awards to DNAngel

Popular Question 8 months ago, created a question with more than 1,000 views. For makeblastdb.exe giving me an unclear error message when creating a database
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