User: little_more

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little_more20
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Posts by little_more

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Comment: C: Is there a database with calculated Ka/Ks ratios for human/mouse genomes?
... Yes, I've already found it. Thank you very much! ...
written 3 months ago by little_more20
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Comment: C: Is there a database with calculated Ka/Ks ratios for human/mouse genomes?
... But BioMart provides only a list of orthologs and not pre-calculated Ka/Ks ratios, doesn't it? ...
written 3 months ago by little_more20
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Is there a database with calculated Ka/Ks ratios for human/mouse genomes?
... The header pretty much sums up my question. I need (somehow calculated) Ka/Ks ratios for human/mouse genomes. Is there any database with calculated ratios for each ortholog? Otherwise, maybe someone knows an article with a table where the ratios for all orthologs are listed? Or do I need to collect ...
database evolution written 3 months ago by little_more20
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Comment: C: bwa parallel on a SLURM cluster
... I see. Thanks very much for your help! ...
written 6 months ago by little_more20
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Comment: C: bwa parallel on a SLURM cluster
... I see. so every task will run on a separate CPU and a node needs to have 34 CPUs? ...
written 6 months ago by little_more20
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Comment: C: bwa parallel on a SLURM cluster
... so you suggest using: #SBATCH --nodes=1 #SBATCH --ntasks-per-node=8 parallel -j 2... right? sorry for many questions I just started working with this cluster and I was surprised when `parallel -j ` ran longer than just `parallel` ...
written 6 months ago by little_more20
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Comment: C: bwa parallel on a SLURM cluster
... [ATpoint][1], thanks for answering to *my* question without endless referring to snakemake! :) clusters specifications: 376 nodes: each with 2 processors (8 cores each) & 64 GB RAM 144 nodes: each with 2 processors (12 cores each) & 64 GB RAM do you specify how much memory you need wit ...
written 6 months ago by little_more20
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bwa parallel on a SLURM cluster
... I'm working on a SLURM cluster with NGS data. I trimmed raw reads and was thinking of the best way to align them to the reference genome. I have pairs of reads for a few samples. I wrote a script for parallel bwa: #SBATCH --cpus-per-task=1 #SBATCH --ntasks=10 #SBATCH --nodes=1 # al ...
bwa written 6 months ago by little_more20
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Comment: C: bwa mem: fail to locate the index files
... it works now, thank you very much! ...
written 7 months ago by little_more20
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bwa mem: fail to locate the index files
... Hi all, I have a problem with running bwa in parallel. I'm using this script (as kindly suggested in [this topic][1]): # reference hg1kv37=/dir/to/reference/and/index/files/human_g1k_v37.fasta # create a function bwatosam() { id="$1" bwa mem -t 10 -R "@RG\tID ...
bwa written 7 months ago by little_more20 • updated 7 months ago by ole.tange3.7k

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