User: goatsrunfaster

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Posts by goatsrunfaster

<prev • 41 results • page 2 of 5 • next >
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Comment: A: Looking for easy to use eukaryotic genome annotation pipeline?
... Using maker seems like the way to go, thanks for the info! ...
written 8 weeks ago by goatsrunfaster20
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Looking for easy to use eukaryotic genome annotation pipeline?
... I am trying to annotate a eukaryotic genome but every pipeline I find seems convoluted and complex. All I really have is a fish assembly in fasta format. I am simply looking for pipeline suggestions, ideally that I can install with conda, that also have an easy to understand tutorial. I usually work ...
assembly written 8 weeks ago by goatsrunfaster20
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Answer: A: fasterq-dump not splitting files?
... Nevermind, my mistake, its working. ...
written 10 weeks ago by goatsrunfaster20
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Answer: A: exclude variants based on position in vcf file
... Figure it out: vcftools --vcf cluster_1_private.vcf --exclude-positions remove_poly_1.txt --recode --recode-INFO-all --out cluster_1_fixed text file needs to be a tab-separated list of chromosome and positions ...
written 6 months ago by goatsrunfaster20
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exclude variants based on position in vcf file
... I have a list of positions (POS) in a text file I would like to remove from a .vcf file. What is the simplest way to do this? I have tried: vcftools --vcf cluster_1_private.vcf --exclude remove_poly_1.txt --recode --recode-INFO-all --out cluster_1_fixed but this doesnt seem to work, but note the t ...
snp written 6 months ago by goatsrunfaster20
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Comment: C: Remove polymorphic SNPs from VCF file
... For example with the following VCF: Chromosome 1 . T G . PASS AC=5;AN=5 GT 1 1 1 1 1 Chromosome 2 . T C . PASS AC=5;AN=5 GT 1 1 1 1 1 Chromosome 3 . C T . PASS AC=2;AN=5 GT 0 0 1 1 0 Chromosome 4 . G T . PASS AC=5;AN=5 GT 1 1 1 1 1 I want to keep Chromosomes like 1, 2, and 4, but exclude thos ...
written 6 months ago by goatsrunfaster20
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Remove polymorphic SNPs from VCF file
... I have a vcf file I filtered based on groups, and now I want to filter it again so it only contains fixed differences from the reference (e.g. remove all polymorphic loci within the set). Is there a straightforward way to do this? ...
snp written 6 months ago by goatsrunfaster20
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minimum contig size in partial eukaryotic assembly
... I have a eukaryotic genome assembly with a lot of smaller contigs (many in the 150bp range). I would like to remove smaller contigs but wasn't sure of the appropriate size. That being said what is the norm in terms of small contig removal for eukaryotic genomes? Note that this is only a partial asse ...
genome assembly written 8 months ago by goatsrunfaster20 • updated 8 months ago by JC12k
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Comment: C: How to annotate eukaryotic genome
... great thanks, helpful information! ...
written 8 months ago by goatsrunfaster20
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How to annotate eukaryotic genome
... I have a fragmented eukaryotic genome (contigs in fasta format) I would like to annotate (and create a genbank file for if possible). I found The NCBI Eukaryotic Genome Annotation Pipeline page on NCBI, but incredibly I see no information on how to actually run something through that pipeline (I ass ...
genome assembly written 8 months ago by goatsrunfaster20

Latest awards to goatsrunfaster

Scholar 6 months ago, created an answer that has been accepted. For A: Lositan, He and Microsats (expected heterozygosity measures plot higher than exp
Scholar 10 months ago, created an answer that has been accepted. For A: Lositan, He and Microsats (expected heterozygosity measures plot higher than exp

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