User: skbrimer

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skbrimer390
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390
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United States
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4 hours ago
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2 years, 9 months ago
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Posts by skbrimer

<prev • 151 results • page 1 of 16 • next >
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Answer: A: Need help reading FASTQ file
... If it is not a homework question you could use biopython from Bio import SeqIO for seqrecord in SeqIO.parse("file.fastq", "fastq"): print(seqrecord.seq) ...
written 4 days ago by skbrimer390
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Comment: C: SnpEff Custom DB for Recombinant virus
... Sure will! Thank you for the help! ...
written 4 days ago by skbrimer390
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Comment: A: SnpEff Custom DB for Recombinant virus
... The short answer is make sure you do all the steps in the documentation. Boy do I feel silly. ...
written 4 days ago by skbrimer390
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Comment: C: SnpEff Custom DB for Recombinant virus
... You are correct, I forgot to edit the `snpeff.config` file. I had the files in the data dir just forgot to do step two. ...
written 4 days ago by skbrimer390
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SnpEff Custom DB for Recombinant virus
... Good Morning Hive mind, I am using SnpEff v4 to attemp to make a custom database of a recombinant virus we made in house. I have annotated the genome using DNAStar SeqNinja which uses Mauve to map genes from a reference to your genome and then outputs a genbank file. So I have my file, FW200_Ann ...
genome snp written 4 days ago by skbrimer390
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MLST ST Interpretations
... Hello Hive mind, I know it's the weekend and all but I'm going to try anyway. Earlier I posted about sequencing several strep suis genomes and had issues with alignment. I got some good advice to use Mauve which helped a lot still not done with it and I need to go and update that post as well. Any ...
ngs mlst written 12 weeks ago by skbrimer390
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Comment: C: Streptococcus genome alignments
... Thank you for the link! ...
written 3 months ago by skbrimer390
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Comment: C: Streptococcus genome alignments
... Also, and I suspect unsurprisingly (yey circular genomes), it looks like the start of the genome and the end of the genome is in one contig of the de novo build. ...
written 3 months ago by skbrimer390
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Comment: C: Streptococcus genome alignments
... The Mauve alignment shows lots of gene shuffling, this was a great idea! Is it possible to use this alignment to order the contigs? ...
written 3 months ago by skbrimer390
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Comment: C: Streptococcus genome alignments
... Sorry, I am using BWA as the mapper and SPAdes as the de novo assembler. TMAP is a variant of BWA and I do use both. I have found that they give only slightly different builds since the read quality of Ion Torrent has improved. For most builds I do use BWA over TMAP mostly due to the speed. There ar ...
written 3 months ago by skbrimer390

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Popular Question 4 days ago, created a question with more than 1,000 views. For Can Q10 be better than Q30
Teacher 4 days ago, created an answer with at least 3 up-votes. For A: Thrown Into A Bioinformatics Position
Scholar 4 days ago, created an answer that has been accepted. For A: Submitting several BLAST queries using NCBIWWW at once
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Scholar 4 months ago, created an answer that has been accepted. For A: Submitting several BLAST queries using NCBIWWW at once
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Scholar 17 months ago, created an answer that has been accepted. For A: Submitting several BLAST queries using NCBIWWW at once
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