User: skbrimer

gravatar for skbrimer
skbrimer430
Reputation:
430
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Location:
United States
Last seen:
5 days, 3 hours ago
Joined:
2 years, 11 months ago
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Posts by skbrimer

<prev • 156 results • page 1 of 16 • next >
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Comment: C: uniprot embl Ncbi
... Good point. I forgot that. It is a good manual though. I feel it was well worth the money. ...
written 9 days ago by skbrimer430
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Comment: C: How to deal with Segmentation fault in BWA?
... A lot of times this is an issue with the index, try rebuilding the index files and rerunning the alignment. ...
written 9 days ago by skbrimer430
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Comment: C: uniprot embl Ncbi
... Oh! I completely overlooked the best help for beginners. You can read the Biostars handbook which includes a section on where and how to get data https://www.biostarhandbook.com/data/where-to-get-data.html ...
written 9 days ago by skbrimer430
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Answer: A: uniprot embl Ncbi
... Not to be mean, however this is a really poor question and the answers, if you get them at all, will most likely be very unhelpful. However to at least point you in a direction. In general they all have ftp sites for bulk downloads or a link to download (in whatever format you need) next to the file ...
written 9 days ago by skbrimer430
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Answer: A: Download all NCBI gene names, synonyms, and gene ID for an organism
... Do you mean, you would like to download the complete reference from NCBI from the RefSeq FTP site? like here for [mouse][1] and her for [human][2] [1]: ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Mus_musculus/reference/GCF_000001635.26_GRCm38.p6 [2]: ftp://ftp.ncbi.nlm.nih. ...
written 5 weeks ago by skbrimer430
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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 9 weeks ago by skbrimer430
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Comment: C: SnpEff Custom DB for Recombinant virus
... Sure will! Thank you for the help! ...
written 9 weeks ago by skbrimer430
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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 9 weeks ago by skbrimer430
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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 9 weeks ago by skbrimer430
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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 9 weeks ago by skbrimer430

Latest awards to skbrimer

Popular Question 9 weeks ago, created a question with more than 1,000 views. For Can Q10 be better than Q30
Teacher 9 weeks ago, created an answer with at least 3 up-votes. For A: Thrown Into A Bioinformatics Position
Scholar 9 weeks ago, created an answer that has been accepted. For A: Submitting several BLAST queries using NCBIWWW at once
Popular Question 4 months ago, created a question with more than 1,000 views. For Can Q10 be better than Q30
Popular Question 5 months ago, created a question with more than 1,000 views. For Can Q10 be better than Q30
Scholar 6 months ago, created an answer that has been accepted. For A: Submitting several BLAST queries using NCBIWWW at once
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Scholar 19 months ago, created an answer that has been accepted. For A: Submitting several BLAST queries using NCBIWWW at once
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