User: jean.elbers

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jean.elbers290
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Posts by jean.elbers

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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 2 days ago by jean.elbers290
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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 6 weeks ago by jean.elbers290
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Answer: C: how to analyze synteny between 4 genomes. please suggest suitable tool
... https://github.com/rhysf/Synima ...
written 6 weeks ago by jean.elbers290
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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 7 weeks ago by jean.elbers290
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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 8 weeks ago by jean.elbers290
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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 8 weeks ago by jean.elbers290
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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 8 weeks ago by jean.elbers290
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Comment: C: How to perform KaKs_Calculator from SNPEff's output
... 1. KaKs_Calculator requires ***sequences*** in the .axt format not SNPs. 2. What is the goal of using KaKs_Calculator? ...
written 9 weeks ago by jean.elbers290
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Comment: C: bedtools getfasta (how to get only cds coding sequence)
... Have you tried gffread - part of gff utilities (http://ccb.jhu.edu/software/stringtie/gff.shtml)? ...
written 3 months ago by jean.elbers290
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Answer: A: Reference Guided De Novo assembly of Contigs generated from Illumina PE Reads
... Ragout (https://github.com/fenderglass/Ragout) is also another option. ...
written 3 months ago by jean.elbers290

Latest awards to jean.elbers

Teacher 25 days ago, created an answer with at least 3 up-votes. For A: What is Read Group platform??
Teacher 4 weeks ago, created an answer with at least 3 up-votes. For A: What is Read Group platform??
Scholar 3 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 3 months ago, created an answer with at least 3 up-votes. For A: What is Read Group platform??
Scholar 4 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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