User: truebeliever24

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Posts by truebeliever24

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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 8 days ago by truebeliever2420 • updated 7 days ago by Brice Sarver2.8k
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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 8 days 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 17 days 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 8 weeks ago by truebeliever2420 • updated 8 weeks ago by zx87548.0k
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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 10 weeks 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 11 weeks ago by truebeliever2420
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Comment: C: pulling out a single pseudochromosome from my vcf file
... I've supplied what I think is the correct information below. Would you mind helping me correcting my expression? I believe it is something close to the following: grep -v -w '^#\|^#CHROM\|^chr[Z]' selas.dp1maxmiss50maf05f_subset_.012.vcf > Z.vcf Thanks! ##fileformat=VCFv4.2 ##FIL ...
written 11 weeks ago by truebeliever2420 • updated 11 weeks ago by genomax70k
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Comment: C: pulling out a single pseudochromosome from my vcf file
... I'm not entirely sure. I don't have a vcf file with chromosomes labeled that would fit as "chr". Only the vcf file with Pseudochromosomes, so I can't really test whether the original line works. I got the line from here: https://www.biostars.org/p/201603/ I just tried this: grep -v -w '^#\|^#CHROM\ ...
written 11 weeks ago by truebeliever2420
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Comment: C: pulling out a single pseudochromosome from my vcf file
... Thanks for the reply. Unfortunately, that is not working for me. When I add "-v", the new file is the same size as the original vcf. I want a new vcf file that will contain only the Z chromosome. When I try without "v", the new file is only 10kb, tiny and containing no information besides a chromoso ...
written 11 weeks ago by truebeliever2420
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pulling out a single pseudochromosome from my vcf file
... Hi everyone, I am trying to extract a single chromosome from my dataset so that I can run analyses using only this sex chromosome and compare to results of similar analyses on the entire genome. However, all of my chromosomes are labeled as "Pseudochromosomes", i.e., the chromosome I want to extrac ...
genome written 11 weeks ago by truebeliever2420 • updated 11 weeks ago by genomax70k

Latest awards to truebeliever24

Scholar 5 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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