User: truebeliever24

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Posts by truebeliever24

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Bioinformatics computer upgrade help
... Hi all, I am trying to upgrade my Windows 10 computer so that I can work with genomic data/do analyses with whole genome data, manipulate large text files (several gigabytes), edit figures that are several MB in Illustrator. With my current setup (below), I'm unable to do these things. My setup: ...
computer upgrade written 1 day ago by truebeliever2420 • updated 21 hours ago by zx87549.4k
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manhattan plots with nucleotide diversity and dxy estimates
... Hi everyone, Sorry for the ignorant question, but I want to create two separate manhattan plots for whole genome data (SNPs), one using dxy estimates and one using pi estimates across all of the chromosomes. I have these data in hand for each window, but I don't know how to calculate the p-values t ...
genome selection manhattan plot written 3 days ago by truebeliever2420
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Comment: C: bwa mem - expected runtime?
... The read files are on the cluster server-as far as I know, I am not using an NFS share. I'm running the following (so I don't think I'm piping to samtools-I am outputting a sam file directly): bwa mem -t 24 $ref $i.fastqsanger > $i.sam done then I plan to run the following: # SAM t ...
written 10 months ago by truebeliever2420 • updated 10 months ago by RamRS27k
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bwa mem - expected runtime?
... Hi everyone, I am running an alignment to the Anna's Hummingbird reeference genome using files of 10 runs that range from 7.6 to 10.2 Gb in size, and 2.2-2.9 giga bases in length. I am using the command bwa mem -t 24, running on a cluster, using 24 cpus and 12 gb of memory per cpu (the max I coul ...
alignment written 10 months ago by truebeliever2420
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genome mapping help requested
... Hi everybody, I'm struggling heavily with the following, and could use some in-depth help, perhaps over message or chat (I'd be happy to pay you for your time), with the following: I have a dataset of whole genomes for 134 individuals of two species, one of the two species has two subspecies. I wa ...
alignment written 10 months ago by truebeliever2420 • updated 10 months ago by Brice Sarver3.5k
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Comment: A: obtaining fastq files from NCBI
... Thanks for the reply. I have a set of genomes for two species aligned to the Anna's genome. I want to make a phylogeny, using Anna's as the outgroup, so I am trying to obtain raw reads of Anna's Hummingbird to align to the Anna's genome. Is raw read data available somewhere? I've been trying for a ...
written 11 months ago by truebeliever2420
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obtaining fastq files from NCBI
... Hi everyone, I am trying to download a genome in the fastq format, but can only access the fasta format to this point. I know that I can use the SRAtoolkit to convert SRA format to fastq, but I'm not sure which genome to choose, or even if these are entire genomes. For example, when I search "Caly ...
genome ncbi sratoolkit written 11 months ago by truebeliever2420
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kmer analysis for sequences of behavior
... Hi all, I have been trying to use kmer analysis (using k=3) to identify phenotypes of behavioral sequences. For example, if each letter is a behavior within a courtship display, I could have the following: Species A: R R R R R S H E Species B: P P P P P P A S H E Hybrid 1: P P P P R R ...
R written 12 months ago by truebeliever2420 • updated 12 months ago by zx87549.4k
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Comment: C: pulling out a single pseudochromosome from my vcf file
... Thank you for your help! This resolved the issue. ...
written 13 months ago by truebeliever2420
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Comment: C: pulling out a single pseudochromosome from my vcf file
... Thanks! I've made some progress now! I was able to compress and index the vcf file, and this command (bcftools view input.vcf.gz --regions Pseudochromosome_Z) worked, allowing me to view the Z chromosome. How can I save a separate vcf file with only the information from the Z chromosome? ...
written 13 months ago by truebeliever2420

Latest awards to truebeliever24

Scholar 15 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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