User: LRStar

gravatar for LRStar
LRStar20
Reputation:
20
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New User
Location:
United States
Last seen:
1 day, 23 hours ago
Joined:
5 years, 10 months ago
Email:
l**********@gmail.com

about me

Posts by LRStar

<prev • 28 results • page 1 of 3 • next >
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Comment: C: Chromosome alignment visualization and gene elicitation for bacterial samples wi
... @Carambakaracho. Thank you for your help. I found the sourmash tool to be a useful resource I did not previously know about. I indeed followed your helpful advice and downloaded all Helicobacter genomes (n=211) and then ran various k-mer signatures to determine relatedness. The first sample matched ...
written 6 days ago by LRStar20
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Comment: C: Finding a specific gene in a fastq file without mapping the reads?
... @lh3 and @JorgeAmigo: This might be a simple question, but how would this two-step process be accomplished (in terms of input and output files)? I have a gene of interest called vaca (vacuolating cytotoxin), which has about 3873 base pairs (https://www.ncbi.nlm.nih.gov/nuccore/NC_000915.1?report=fas ...
written 9 days ago by LRStar20
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Comment: C: Chromosome alignment visualization and gene elicitation for bacterial samples wi
... @Carambakaracho Thank you for your suggestions and I am researching them now. Can I clarify what you mean about going "with proteins from the predictions"? Would this approach not require reference genome? What software/procedure would I use to generate these predictions (i.e. predictions of protein ...
written 9 days ago by LRStar20
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Chromosome alignment visualization and gene elicitation for bacterial samples with unknown reference genomes
... This is a somewhat of a follow-up from a previous post (https://www.biostars.org/p/397137/). I was recently given 4 paired-end .fastq files (where each read has about 150 bases), each from a different strain of bacteria. The researchers seem to expect these 4 samples to likely be from the same genre ...
gene assembly alignment muave bacteria written 9 days ago by LRStar20
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Comment: C: Assemble bacterial .fastq files and find differences (SPAdes followed by MUMmer)
... Thank you for your helpful response @Joe. My advisor is looking into finding out more about the samples but believes they are likely from the same strain. As a result, I blasted some of the contigs from the sample and downloaded a possible reference genome (I'll call it h.fasta here). I tried/rese ...
written 11 days ago by LRStar20
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Assemble bacterial .fastq files and find differences (SPAdes followed by MUMmer)
... This is somewhat of a follow-up from a previous post (https://www.biostars.org/p/395813/). I was recently given 4 paired-end .fastq files (where each read has about **150 bases**), each from a different strain of bacteria. My assignment is to 1) assemble each strain into its full circle and 2) perfo ...
spades mummer bacteria contig snp written 17 days ago by LRStar20 • updated 17 days ago by Joe14k
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Assemble bacterial .fastq files and find differences in insertions, deletions, and duplications
... I was recently given 4 paired-end .fastq files, each from a different strain of bacteria. I was told each .fastq file should have about 50 contigs and that each contig should have a length <200KB with read depths of about 40. My assignment is to 1) assemble each strain into its full circle and 2) ...
insertions assembly bacteria deletions written 26 days ago by LRStar20 • updated 26 days ago by swbarnes26.5k
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Functional annotation chart from DAVID: Analogs or direct affiliations?
... I am trying to determine if genes I am examining are honey bee affiliations or are human analogs. Basically, I: 1) Went to the DAVID bioinformatics software (https://david.ncifcrf.gov/). 2) Used "functional annotation" option. 3) Input a list of BeeBase IDs (all beginning with "GB", such as "GB ...
annotation david functional written 7 months ago by LRStar20
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Comment: C: Mapping metagenome information to amplicon sequences
... Thanks for your advice! I did now use **bowtie2 --sensitive-local** for my samples (n=35). The 35 samples varied widely in terms of their total alignment, ranging between 0.09% and 94% alignment! Much of the reads that aligned did so to more than one location, with 1-time alignment ranging between ...
written 13 months ago by LRStar20
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Mapping metagenome information to amplicon sequences
... Hello all, I have a set of amplicon sequences for antimicrobial resistance determinants. Each amplicon sequence varies in length between 125 and 275 bp. I also have a .fastq file with metagenomic reads. Each metagenomic read varies in length between 25 and 473 bp. I would like to map the amplico ...
ampliseq mapper written 13 months ago by LRStar20 • updated 13 months ago by btsui290

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