User: truebeliever24

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Posts by truebeliever24

<prev • 32 results • page 1 of 4 • next >
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psmc bootstrapping help
... Hi all, I'm having trouble bootstrapping with psmc. I am able to run the analysis without bootstrapping and generate the plot, but I can't seem to get it going correctly with bootstrapping. I'd like to do 100 replicates. Here's the code I've tried: seq 100 | xargs -P 6 psmc -N25 -t15 -r5 -p "4+25 ...
psmc bootstrap written 10 days ago by truebeliever2420
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Comment: A: psmc bootstrap plotting?
... Would anyone mind sharing the code they used to generate the psmc bootstraps? I'd appreciate it, as I'm struggling with that step! Thanks ...
written 10 days ago by truebeliever2420
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Comment: A: change name of scaffold to chromosome in .bam file
... Any help is appreciated. ...
written 5 weeks ago by truebeliever2420
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change name of scaffold to chromosome in .bam file
... Hi, I have scaffold level data, and I know the chromosomal assignment of each scaffold, and am trying to rename each scaffold to each chromosome it belongs to. Here's the command I tried to rename one scaffold to chromosome 1 as a test: samtools view -h s2907.bam |sed -e 's/SN:QRBIO1000092.1/SN: ...
genome written 5 weeks ago by truebeliever2420 • updated 5 weeks ago by seidel7.4k
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--max-missing filter in vcftools removes most of my SNP data
... Hi everyone, I am doing some variant calling in vcftools using the command below, and have noticed that the --max-missing function removes most of my data (it trims the vcf file from 32gb to 9kb). Dropping --max-miss to 0.8 raises the output file to 21.1 mb. What could be going on here? Any help is ...
genome missing max vcftools snp written 8 weeks ago by truebeliever2420
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help with calling invariant sites in parallel: scaffolds not present in all bam files are skipped
... Hello, I'm using bcftools to call invariant sites in parallel. It appears that only scaffolds that are present across all bam files are included, while any scaffold missing in an individual in the dataset is omitted. What can I do to ensure all scaffolds are included in the invariant site calling? ...
invariant bam bcftools scaffold written 11 weeks ago by truebeliever2420
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need to map scaffolds to chromosomes: have mashmap outfile
... Hi, I have many genomes that are aligned to a reference genome composed entirely of scaffolds. I used mashmap to produce the mappings of these scaffolds to a fully sequenced, close relative that has chromosomes assigned (mashmap.out file). Now I need to use the mapping output from mashmap to actual ...
mashmap scaffold chromosome written 3 months ago by truebeliever2420
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Help with environmental niche model
... HI everyone, For downstream analyses I want to correlate genetics of two subspecies with differences in the environment across geographic space, but first I need help in planning of my niche models. I have two subspecies that I need to make niche models for that are not possible to differentiate b ...
genes environmental niche model written 3 months ago by truebeliever2420
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Comment: C: Bioinformatics computer upgrade help
... I will give this a try, thank you. I need to be able to remove hundreds of columns of missing data for over 100 individuals, and it's been pretty awful dealing with that. I've tried nano (and that is all I am really aware of), and it's not easy visualizing the data and observing what I need to take ...
written 7 months ago by truebeliever2420
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Comment: C: Bioinformatics computer upgrade help
... I tried Linux and it was still rather slow for me (although I had to install it on an HDD-I didn't have adequate space on my small SSD). Whatt do you think of the following upgrades, and then installing Linux (the GUIs I need are available on Ubuntu Desktop)? AMD Ryzen Threadripper 3970x 32-core pr ...
written 7 months ago by truebeliever2420

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Popular Question 12 days ago, created a question with more than 1,000 views. For bwa mem - expected runtime?
Scholar 23 months ago, created an answer that has been accepted. For A: ls function in windows bash terminal not showing all files

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