User: goatsrunfaster

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4 years, 4 months ago
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Posts by goatsrunfaster

<prev • 37 results • page 1 of 4 • next >
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looking for a way to identify a specific gene, and in varying numbers across multiple genomes.
... I am looking for a way to identify a gene (or more specifically a sequence), and the number of those sequences across a number of bacterial isolates. Assuming I have the sequence. What is the best way to do that? Are there any tools specifically built for finding a user-supplied sequence across a la ...
gene written 12 days ago by goatsrunfaster20 • updated 12 days ago by oakhamwolf20
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Answer: A: Problems setting up nt blast database
... I figured it out, I didnt realize the -db option had to be the .nal file name (which in this case was env_nt) ...
written 15 days ago by goatsrunfaster20
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Problems setting up nt blast database
... I am pulling my hair out trying to simply set up blast on my university server system. I downloaded all 36 of the packaged nt database files from the ncbi ftp site (nt.00-nt.35), and put them in the following folder: `/network/rit/lab/andamlab/bin/ncbi-blast-2.10.1+/blast/db` I then added this pat ...
software error written 15 days ago by goatsrunfaster20
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Comment: C: extract single contig from fasta file based on name?
... Its not a file, its just the name of the contig. I am looking for way to do this with just the name of a contig rather than using a file, that is the whole point of this post. ...
written 26 days ago by goatsrunfaster20
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Comment: C: extract single contig from fasta file based on name?
... If I was able to extract a single contig based on its name with seqtk it would look like this: seqtk subseq in.fq contig00001 > out.fq but I cannot do that because it actually requires a list, and must look like this: seqtk subseq in.fq name.lst > out.fq Given that I have hundreds of fasta ...
written 26 days ago by goatsrunfaster20
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extract single contig from fasta file based on name?
... I would like to extract a single contig from a fasta file, and I have many fasta files and contigs I need to do this with. Note the fasta files have different names and the contigs have different names for each scenario. I know I can use seqtk with a list, but building a list for each assembly is a ...
assembly written 27 days ago by goatsrunfaster20 • updated 23 days ago by harishk020170
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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 27 days 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 27 days ago by goatsrunfaster20
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Answer: A: fasterq-dump not splitting files?
... Nevermind, my mistake, its working. ...
written 5 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 5 months ago by goatsrunfaster20

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