User: Kevin

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Kevin630
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Posts by Kevin

<prev • 46 results • page 1 of 5 • next >
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Comment: A: Mira assembler with IonTorrent
... Please refrain from making duplicate posts https://www.biostars.org/p/385156/ ...
written 5 months ago by Kevin630
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Comment: A: Help in Gwas analysis
... maybe slightly off topic but if you are new to GWAS and Affy you may wish to take note of this http://www.affymetrix.com/support/help/faqs/dna_ge_arrays/faq_32.jsp ...
written 6 months ago by Kevin630
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Comment: A: parse of file multifasta in python
... any reason you didn't try https://biopython.org/wiki/SeqIO? ...
written 8 months ago by Kevin630
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Answer: A: 16S rRNA classification pipeline
... one point of reference/ comparison is running the 16s workflow in https://ionreporter.thermofisher.com using their supplied demo data. Their panel uses more regions than your data, but the data visualisations should inspire you to do more. i don't think de novo assembly will add new information bu ...
written 10 months ago by Kevin630
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Answer: A: Pool Whole Genome Sequencing
... Can I double check what do you mean by pool? There's making individual libraries for every sample but I am wondering if you mean to mix the DNA of the individual fishes in a pool for WGS to survey the genome. Fishes can have a rather large genome size. The nextseq can generate 120 gb of data Ion ...
written 15 months ago by Kevin630
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Answer: A: Creating A New File by Combining Two Separate Files
... might need to loop twice, once to create a new column that's conditional on the 2nd column then using https://stackoverflow.com/questions/37697195/how-to-merge-two-data-frames-based-on-particular-column-in-pandas-python to create your final output file? perhaps inefficient but how many rows do you ...
written 20 months ago by Kevin630
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Comment: C: randomly subsampling a bam file three times
... in case it's not apparent , PROBABILITY=Double P=Double The probability of keeping any individual read, between 0 and 1. Default value: 1.0. This option can be set to 'null' to clear the default value. use 0.25 for ~ 25% of the reads. ...
written 2.3 years ago by Kevin630
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Answer: A: Where Can I Find Data Setnormal\Tumor Of Cancer?
... Other possible sources which have other kinds of datasets European Genome-phenome Archive https://www.ebi.ac.uk/ega/datasets EGAD00001000082 20 Matched Pair Breast Cancer Genomes Illumina HiSeq 2000, Illumina Genome Analyzer II 42 bam https://www.ebi.ac.uk/ega/datasets/EGAD00001000082 https://dis ...
written 3.0 years ago by Kevin630
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Answer: A: 10Kb Reads From Illumina Hiseq
... The first set of public data is out already. they have 3000 8500bp reads (single end) http://kevin-gattaca.blogspot.sg/2013/07/what-would-you-do-with-3k-of-8500-bp.html ...
written 6.3 years ago by Kevin630
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Convert Illumina Human Hapmap 550 K Chip Manifest File From B36 To B37
... Hi I have old data that was genotyped on convert Illumina Human Hapmap 550 k chip the old manifest file is in b36. What's the best way to migrate this info to b37? I know one approach was to use bwa to align the probes and annotating the sam file. But I googled and can't find a tool that does t ...
illumina convert written 7.2 years ago by Kevin630 • updated 7.2 years ago by Istvan Albert ♦♦ 81k

Latest awards to Kevin

Epic Question 20 months ago, created a question with more than 10,000 views. For Best Practices / Faster Samtools Mpileup, Any Tips?
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Great Question 3.0 years ago, created a question with more than 5,000 views. For Best Practices / Faster Samtools Mpileup, Any Tips?
Good Question 3.0 years ago, asked a question that was upvoted at least 5 times. For Where Can I Download Vcf Files For Publicly Available Data?
Popular Question 3.6 years ago, created a question with more than 1,000 views. For How To Extract Snps From A Desired List Of Gene Names
Appreciated 6.3 years ago, created a post with more than 5 votes. For Where Can I Download Vcf Files For Publicly Available Data?
Great Question 6.3 years ago, created a question with more than 5,000 views. For Best Practices / Faster Samtools Mpileup, Any Tips?
Good Answer 6.3 years ago, created an answer that was upvoted at least 5 times. For A: Is There Any R Or R / Bioconductor Package That Can Make Circular Plots Like Per
Popular Question 6.3 years ago, created a question with more than 1,000 views. For Bwa Aln -Q 15 When To Use It? What Does It Do?
Popular Question 6.3 years ago, created a question with more than 1,000 views. For How To Extract Snps From A Desired List Of Gene Names
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Popular Question 6.3 years ago, created a question with more than 1,000 views. For Where Can I Download Vcf Files For Publicly Available Data?
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Popular Question 6.3 years ago, created a question with more than 1,000 views. For Putting Run/Lane Info Back Into Readgroup For Gatk Pipeline
Popular Question 6.3 years ago, created a question with more than 1,000 views. For How To Create Genome-Wide Estimation Of Ibd Sharing Using Plink From Tped Files?

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