User: hdy

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hdy90
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Posts by hdy

<prev • 23 results • page 1 of 3 • next >
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multiple trees returned from BEAST2
... I have my sequences aligned and put it into beast 2 to get phylogenetic tree. But the returned NEXUS tree file contains so many trees (~10k). What should I do? Are those trees equally good? I have already used MCMC to be 1 million. Should I just increase the MCMC chain length or should I run other p ...
phylogeny phylogenetic tree written 2.2 years ago by hdy90
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phylogenetic tree with known sampling date prior
... I have an experiment which provides sequencing data for the bacteria at different sample time point. Normally when plotting the phylogenetic tree after multi-sequence alignment, the resulted tree is a representation of all the genomes collected without the useful prior knowledge of the sampling date ...
phylogeny bayesian phylogenetic tree written 2.2 years ago by hdy90 • updated 2.2 years ago by Brice Sarver2.5k
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Answer: A: Get identical mapped nucleotide length from bowtie2 generated SAM files
... find out the answer in another post: https://www.biostars.org/p/7331/ ...
written 2.6 years ago by hdy90
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Get identical mapped nucleotide length from bowtie2 generated SAM files
... I used bowtie2 to map my reads to a reference genome and get the SAM files returned. I am wondering if there is a way to get the length of the identical mapped nucleotide length. Basically I want to get a hamming distance or identical mapping vs total read length ratio from the SAM files. ...
bowtie2 sequence mapping written 2.6 years ago by hdy90
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Comment: C: download full genebank format sequences from NCBI
... That helps! Thank you! ...
written 2.6 years ago by hdy90
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Comment: C: download full genebank format sequences from NCBI
... for example: http://www.ncbi.nlm.nih.gov/nuccore/BA000007.2 The last line of the downloaded genbank seqeunce file is "ORIGIN", but the complete genbank file should have sequences behind it. The genbank format: http://www.ncbi.nlm.nih.gov/Sitemap/samplerecord.html. It mentioned that "The ORIGIN ma ...
written 2.6 years ago by hdy90
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download full genebank format sequences from NCBI
... How to download gb files that contains the sequences as well? Tried the Genbank and Genbank (full) in NCBI, but both downloaded files stopped at "ORIGIN//" and no further sequences attach below. ...
ncbi written 2.6 years ago by hdy90 • updated 2.6 years ago by dago2.5k
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Comment: C: Blastn high mem usage, very low CPU usage
... So if the database is very large, for example, whole eukaryotic genomes, what people do is to split databases into small pieces and blast the query multiple times and in the end, merge all the results. Is this right? ...
written 2.7 years ago by hdy90
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Comment: C: Blastn high mem usage, very low CPU usage
... three separate ones, bacteria is the largest ~200G, other two is pretty small ...
written 2.7 years ago by hdy90
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Blastn high mem usage, very low CPU usage
... I am doing a blastn search on a local machine (4 cores, 8 threads, 8GB mem). My database is NCBI bacteria, archaea, viral refseq, which is about 200GB. What I noticed now is that the mem usage is very high with 7711M used, ~14M unused, the VM usage is 395G. However, my CPU is in very low usage: 1.6% ...
alignment blast written 2.7 years ago by hdy90 • updated 7 weeks ago by RamRS19k

Latest awards to hdy

Popular Question 2.1 years ago, created a question with more than 1,000 views. For Gi Number To Taxid To Phylum Name
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Gi Number To Taxid To Phylum Name
Great Question 2.5 years ago, created a question with more than 5,000 views. For R use models from survival analysis and do prediction
Scholar 2.6 years ago, created an answer that has been accepted. For A: Get identical mapped nucleotide length from bowtie2 generated SAM files
Popular Question 2.6 years ago, created a question with more than 1,000 views. For Gi Number To Taxid To Phylum Name
Popular Question 3.9 years ago, created a question with more than 1,000 views. For Gi Number To Taxid To Phylum Name
Popular Question 3.9 years ago, created a question with more than 1,000 views. For How To Associate Cpg Coordinate With The Gene Names Or Entrez Id
Popular Question 3.9 years ago, created a question with more than 1,000 views. For R survival analysis
Popular Question 3.9 years ago, created a question with more than 1,000 views. For R use models from survival analysis and do prediction

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