User: Kevin

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Kevin640
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Posts by Kevin

<prev • 47 results • page 1 of 5 • next >
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Comment: C: Protocol for genome assembly of Sars-cov-2 sequences
... is this the ampliseq panel for SARS-CoV-2 ? they have Trinity setup as a torrent suite plug-in that you can use within the software that they provide. ...
written 4 months ago by Kevin640
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Comment: A: Mira assembler with IonTorrent
... Please refrain from making duplicate posts https://www.biostars.org/p/385156/ ...
written 17 months ago by Kevin640
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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 18 months ago by Kevin640
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Comment: A: parse of file multifasta in python
... any reason you didn't try https://biopython.org/wiki/SeqIO? ...
written 21 months ago by Kevin640
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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 22 months ago by Kevin640
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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 2.3 years ago by Kevin640
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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 2.7 years ago by Kevin640
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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 3.3 years ago by Kevin640
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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 4.1 years ago by Kevin640
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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 7.4 years ago by Kevin640

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