User: mike-zx

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mike-zx40
Reputation:
40
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New User
Location:
Mexico/Service of Alimentary Quality SENASICA
Last seen:
7 hours ago
Joined:
1 month ago
Email:
m******@hotmail.com

Posts by mike-zx

<prev • 14 results • page 1 of 2 • next >
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Answer: A: Join/Combine gff3 or gtf files
... cat file1.gff3 file2.gff3 >> combined.gff3 That cat syntax should give you what you want Hope this helps ...
written 17 hours ago by mike-zx40
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Answer: A: How to write a proper bed file to extract sequence?
... bedtools is complaining about your file not being tab-delimited, try the following on your file if you have awk in your terminal to avoid making it again manually with tabs since I'm assuming its a big file: cat pAcr_extract.bed | awk 'BEGIN{OFS="\t";} {print $1,$2,$3;}' > pAcr_extract_tab.b ...
written 1 day ago by mike-zx40
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Comment: C: Extract gene location and gene name from bed file for FASTA file
... Did you try using the `-name` option in the bedtools syntax? If that gives you the gene name in the first column you could add the starting and ending positions of the genes to the bedtools output by yourself with awk. ...
written 2 days ago by mike-zx40
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Answer: A: In silico functional comparison between two strains
... Your question is rather broad, but if you are looking for something general and vast regarding bacterial strains I'd recommend looking into this site: https://www.patricbrc.org/ That platform is really good for bioinformatics starters since it operates fully on a graphic interface; there you can mak ...
written 4 days ago by mike-zx40
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Answer: A: What does it mean when the ident values are lower than the query cover?
... In BLAST ident percentage is the extent to which two aligned sequences have the same exact nucleotides or aminoacids in the same positions, so for short how similar they are qualitatively. Query cover on the other hand is more of a "quantitative" thing, since it expresses how much of your query sequ ...
written 6 days ago by mike-zx40
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Comment: C: Filtering contigs by length during assembly?
... So you mean if you have an average read length of 150 nucleotides (as it is frequent for illumina pair-end reads), you would do it with 300 right? This is something I hadn't thought of. Thank you for your advice. ...
written 6 days ago by mike-zx40
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Answer: A: Fetch gene names from SNP coordinates
... I came up with a scripting solution using bash, linux commands and awk if you want to avoid using BEDtools, also added comments so that you know what is happening: #!/bin/bash for position in $(cat SNPs.file | cut -d' ' -f2) do for scaffold in $(cat SNPs.file | cut -d' ' -f1) ...
written 8 days ago by mike-zx40
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Comment: A: Fetch gene names from SNP coordinates
... I think an example of how your SNPs file looks would be really helpful to solve this. ...
written 13 days ago by mike-zx40
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Comment: C: RefSeq IDs question
... Hello thanks for answering. Yes I'm fetching the tables from RefSeq database and upon your answer I checked how it looks compared to GenBank. For some reason GenBank tables don't have any IDs at all in any of the lines for these 2 columns lol; understandable for refseq accession but they should have ...
written 18 days ago by mike-zx40
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RefSeq IDs question
... Hello, I feel like I'm missing a simple concept or something regarding this: I'm working with NCBI feature table files from bacterial genomes. In this type of tab-delimited text file column 11 and 12 are product_accession and non-redundant_refseq respectively. Most of the lines of the file contain ...
sequence written 19 days ago by mike-zx40

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