User: jerrybug109

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jerrybug10910
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Posts by jerrybug109

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Comment: C: How to check for contamination by one contaminant across multiple whole genome s
... I did blast because after we got the reads back from the core facility I assembled their genomes & aligned contigs to B. subtilis reference with the intention to do some comparative genomic analysis on our 40 samples (they are different strains of B. subtilis, or so we thought at the time). But ...
written 2.7 years ago by jerrybug10910
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Comment: C: How to check for contamination by one contaminant across multiple whole genome s
... Yes, we considered the possibility that perhaps what we sequenced was not what we expected to get. However, I still need to check for contamination. To eliminate the possiblity that a single organism was responsible for cross contamination across 20 samples, couldn't I also do the following: 1. ...
written 2.7 years ago by jerrybug10910
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Answer: A: How to check for contamination by one contaminant across multiple whole genome s
... > Do you mean that ALL of the reads were Bacillus licheniformis, or just some? Were any of the reads from Bacillus subtilis? And specifically, what percent were from each species? And do you happen to know how closely related those species are (in terms of ANI)? Just some. For example, here are ...
written 2.7 years ago by jerrybug10910
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Comment: C: How to check for contamination by one contaminant across multiple whole genome s
... We expected all 40 of our samples to be *Bacillus subtilis*. After we got the short reads from all samples back from the core facility, I BLASTed 10,000 random reads from each sample. 20/40 of the samples got BLAST results that indicated *Bacillus licheniformis*. So I suspect that the *Bacillus lich ...
written 2.7 years ago by jerrybug10910
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Comment: C: How to check for contamination by one contaminant across multiple whole genome s
... > The first thing to do is find out whether everything is contaminated by the same organism, which can be easily accomplished by assembling all of them and then blasting the contigs, or blasting a thousand reads from each sample, and examining the blast hits I've already done this step. We wer ...
written 2.7 years ago by jerrybug10910
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Comment: C: How to check for contamination by one contaminant across multiple whole genome s
... Hi thanks for the suggestion, that looks interesting. In this case would I use a couple of my genomes as the references and see if any of the reads bin "heavily" towards one reference versus the other? Thanks. ...
written 2.7 years ago by jerrybug10910
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How to check for contamination by one contaminant across multiple whole genome sequenced samples?
... Hello Friends, So recently our lab had a batch of different strains of a bacteria whole genome sequenced. We got the short read sequences back from the sequencing facility, and had bit of a surprise. After selecting a random 10k base pairs from each sample and BLASTing them, half of the samples wer ...
bioinformatics alignment genomics sequencing written 2.7 years ago by jerrybug10910
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how to locate a gene sequence among fastq files containing short reads
... Hello! I've got a dozen different strains of bacteria for which we've sequenced the whole genomes of (we have paired end reads - forward and reverse - for each strain). I wish to find and locate a specific house keeping gene in each strain. Could I convert the fastq files into fasta files, set up ...
ncbi bioinformatics blast genome written 2.8 years ago by jerrybug10910 • updated 2.8 years ago by piet1.6k
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Comment: C: how to BLAST search for known genes in local set of genomes?
... Thanks, I appreciate your response. I might give this try then - I have rudimentary UNIX experience. By any chance, do you know of anything like Galaxy that offers service like BLAST but lets you upload your own database? ...
written 3.0 years ago by jerrybug10910
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how to BLAST search for known genes in local set of genomes?
... Hi all, Our lab has sequenced a set of different Bacillus strains and assembled contigs for each individual genome. I wish to set up a search for the presence/absence of multiple known genes (we have FASTA files for those) in our set of genomes. I was hoping to do this via BLAST but looking at the ...
genome ncbi blast bioinformatics written 3.0 years ago by jerrybug10910 • updated 3.0 years ago by natasha.sernova3.4k

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