User: jean.elbers

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jean.elbers340
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Posts by jean.elbers

<prev • 43 results • page 1 of 5 • next >
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Comment: C: estimate dN/dS ratio for multiple genes
... I am not sure what to recommend. I've used the NG model when I have had say one hundred thousand different regions to calculate Ka/Ks for pairwise comparisons. Maybe others will chime in. Sorry. ...
written 6 weeks ago by jean.elbers340
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Comment: C: estimate dN/dS ratio for multiple genes
... See https://www.biostars.org/p/5817/#95075 regarding a comment for using PAML to calculate pairwise dN/dS. I've used KaKsCalculator2 (https://sourceforge.net/projects/kakscalculator2/) for this purpose though. ...
written 7 weeks ago by jean.elbers340
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Comment: C: estimate dN/dS ratio for multiple genes
... I am sorry, but I am not aware of any tools that can calculate dN/dS with the input file you describe. ...
written 9 weeks ago by jean.elbers340
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Comment: C: estimate dN/dS ratio for multiple genes
... I am a little confused by the output of the table as it doesn't seem to indicate the position of the NSY and SYN SNPs? You could potentially generate an alternate reference sequence with BCFtools consensus using the original reference for calling SNPs and the VCF file of variants. You would then nee ...
written 9 weeks ago by jean.elbers340
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Comment: C: Racon-Illumina or Pilon?
... So, this not quite a fair comparison (below) because Pilon was run twice, whilst Racon was only run once, but at least for this data set, Pilon seems to be doing better in terms of few truncated proteins, but I suspect that after an additional round of Illumina-polishing that Racon would be equivale ...
written 3 months ago by jean.elbers340
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Answer: C: how to analyze synteny between 4 genomes. please suggest suitable tool
... https://github.com/rhysf/Synima ...
written 3 months ago by jean.elbers340
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Answer: C: Racon-Illumina or Pilon?
... I am experimenting with that right now to determine whether Racon or Pilon polishing "is better" for an assembly where PacBio reads were used to fill in gaps. Briefly, I get similar assembly statistics, RNAseq mapping rates, indel rates (based on cigar strings and Illumina short-read alignment), and ...
written 3 months ago by jean.elbers340
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Comment: C: Converting a bunch or SRA files using fastq-dump split-files
... What command are you using exactly? It seems to me that fastq-dump wants to include part of the path as individual files. Note sure. It looks like the reads were properly extracted. You can double check by seeing if the number of spots matches the SRA run browser (https://trace.ncbi.nlm.nih.gov/Trac ...
written 4 months ago by jean.elbers340
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Answer: A: Converting a bunch or SRA files using fastq-dump split-files
... 1. You have `'` instead of \` 2. You need `$i` instead of `$f` 3. You need `--split-files` not `-- split-files` for i in \`ls -1 *.sra` ; do ./fastq-dump --split-files $i; done ...
written 4 months ago by jean.elbers340
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Answer: A: Filtering GO terms by neuromuscular processes
... Using the Bioconductor GO.db package, you can query all of the offspring/descendant terms for a GO term (here's an example for the GO term pigment source("http://bioconductor.org/biocLite.R") biocLite("GOstats") biocLite("GO.db") library("GOstats") library("GO.db") example usin ...
written 4 months ago by jean.elbers340

Latest awards to jean.elbers

Teacher 3 months ago, created an answer with at least 3 up-votes. For A: What is Read Group platform??
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: What is Read Group platform??
Scholar 5 months ago, created an answer that has been accepted. For C: bbmap callvariants - how to add sample names, how to get 0/0 alleles back?
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: What is Read Group platform??
Scholar 6 months ago, created an answer that has been accepted. For C: bbmap callvariants - how to add sample names, how to get 0/0 alleles back?

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