User: foxdie

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foxdie0
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Posts by foxdie

<prev • 8 results • page 1 of 1 • next >
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Comment: C: Twobittofa download and install link?
... > twobittofa hg38.2bit hg38.fasta I could not get it to just run like this. Does this have something to do with exporting the path or something (new to this, sorry)? This is what I get: [~/Desktop] >>>>>>>>>> chmod 744 twoBitToFa.dms [~/Desktop] ...
written 4 months ago by foxdie0
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Comment: C: Understand Samtools View Output
... The link is broken for me. ...
written 4 months ago by foxdie0
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Comment: C: How to get a nucleotide at a specified position using a GenBank chromosome acces
... @pbpanigrahi, what do you mean: > following objects are chromosome_name, mouse_dataset are missing ? For reference, I have `mouse_dataset = useDataset("mmusculus_gene_ensembl", mart = ensembl)` if that is what you wanted to know. Let me know if that helps. ...
written 4 months ago by foxdie0
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Comment: C: How to get a nucleotide at a specified position using a GenBank chromosome acces
... (3of3)So, from this I tried to run the following: > getSequence(chromosome = "1", start = 3681267, end = 3681267, upstream = 2, mart = mouse_dataset, seqType = 'cdna', type = 'chromosome_name') ...
written 4 months ago by foxdie0
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Comment: C: How to get a nucleotide at a specified position using a GenBank chromosome acces
... > mouse_dataset@filters[1,] name description 1 chromosome_name Chromosome/scaffold name ...
written 4 months ago by foxdie0
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Comment: C: How to get a nucleotide at a specified position using a GenBank chromosome acces
... (1of3) Hi, thanks for the reply. When I enter: > getSequence(chromosome = "CM000994.2", start = 3681267, end = 3681267, upstream = 2, mart = mouse_dataset, seqType = "cdna", type = chromosome_name) I get a similar `object not found` error again for `type = chromosome_name`: Error in a ...
written 4 months ago by foxdie0
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How to get a nucleotide at a specified position using a GenBank chromosome accession ID with biomaRt?
... **What I have**: I have analyzed a set of WES data with VarScan 2. I now have a somatic variant call .csv with "chrom", "position", "ref", "var", etc. as columns headers. E.g.: chrom position ref var normal_reads1 CM000994.2 3681266 T G 229 CM000994.2 6558171 ...
R biomart bioconductor genbank accession id written 4 months ago by foxdie0
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Comment: C: VarScan and Samtools - how to process my data?
... So does the term "-mpileup" instruct it to take the output of the mpileup before the pipe and use it at that specific place in the varscan command? I'm confused because I'm reading in other places that you can just use a single "-" when piping with SAMtools and it will know to take it as the output ...
written 4 months ago by foxdie0

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