User: skbrimer

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skbrimer440
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5 days, 20 hours ago
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Posts by skbrimer

<prev • 160 results • page 1 of 16 • next >
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Comment: C: QD Annotation error in GATK in VariantRecalibration step
... This link might be helpful https://gatkforums.broadinstitute.org/gatk/discussion/5201/variantrecalibrator-error-values-for-qd-annotation-not-detected-for-any-training-variant I'm guessing you are using a version < GATK 4.0? I don't know alot about it but I tried to recreate your error and the Un ...
written 8 days ago by skbrimer440
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Answer: A: python script to sort blast results and fetch best matches from NCBI
... here is my solution! import re import csv import sys import pandas as pd with open(sys.argv[1], newline="") as csv_file, open("flu_hits.csv","w") as justFlu: reader = csv.reader(csv_file, delimiter="\t") writer = csv.writer(justFlu, delimiter="\t") f ...
written 6 weeks ago by skbrimer440
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Comment: C: python script to sort blast results and fetch best matches from NCBI
... see, this is why I come here. I may have been doing this the hard way ...
written 7 weeks ago by skbrimer440
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python script to sort blast results and fetch best matches from NCBI
... Hello hive mind, I have been trying to automate a process that I do for flu sequencing. I currently use SPAdes to do a de novo build and then blast the contigs using the ncbi command line, remotely. I get back a tab delimited csv file that has the contig, the sequence id, the ncbi acc # and the ra ...
assembly sequence alignment python written 7 weeks ago by skbrimer440
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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 3 months ago by skbrimer440
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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 3 months ago by skbrimer440
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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 3 months ago by skbrimer440
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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 3 months ago by skbrimer440
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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 4 months ago by skbrimer440
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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 5 months ago by skbrimer440

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Popular Question 5 weeks ago, created a question with more than 1,000 views. For Bed file loading issues
Popular Question 6 weeks ago, created a question with more than 1,000 views. For Can Q10 be better than Q30
Popular Question 9 weeks ago, created a question with more than 1,000 views. For Can Q10 be better than Q30
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Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Thrown Into A Bioinformatics Position
Scholar 5 months ago, created an answer that has been accepted. For A: Submitting several BLAST queries using NCBIWWW at once
Popular Question 7 months ago, created a question with more than 1,000 views. For Can Q10 be better than Q30
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Scholar 9 months ago, created an answer that has been accepted. For A: Submitting several BLAST queries using NCBIWWW at once
Popular Question 13 months ago, created a question with more than 1,000 views. For Can Q10 be better than Q30
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Scholar 22 months ago, created an answer that has been accepted. For A: Submitting several BLAST queries using NCBIWWW at once
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Scholar 2.7 years ago, created an answer that has been accepted. For A: Submitting several BLAST queries using NCBIWWW at once
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