User: Jason2

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Jason20
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Posts by Jason2

<prev • 7 results • page 1 of 1 • next >
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How to retrieve all variants for a gene using myvariant.info?
... I really like the information that the [myvariant.info][1] tool can provide, namely annotating the SNPs within genes. I would like to retrieve all of the annotations for a handful of individual genes in R. For instance, in the example API url http://myvariant.info/v1/query/?q=dbnsfp.genename:BTK ...
myvariant.info annotation snp gene genome written 4 months ago by Jason20 • updated 3 months ago by arup1.5k
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Comment: C: How can I parse a json file from MobiDB to retrieve proteome data?
... Thanks! However, I really need to do this for the proteome so hard coding each protein would be difficult. Is there a way to loop over each protein in a high throughput manner? ...
written 6 months ago by Jason20
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How can I parse a json file from MobiDB to retrieve proteome data?
... I've downloaded the mobidb database human data in its json format. It contains protein disorder information for regions of each protein. The issue I'm having is converting the json format nested structure into a table. The file can be downloaded here [click on "json" next to human][1] Here's an ex ...
annotation database format proteins parsing written 6 months ago by Jason20 • updated 5 months ago by ieuangw0
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Comment: C: Finding Frequent To Rare Codon From The Codon Table Of Human
... Sorry I'm late to the party, but do you know of a paper that describes this phenomena? ...
written 2.2 years ago by Jason20
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Comment: C: EdgeR TMM normalisation
... Any questions relating to edgeR may be best answered via the mailing list. http://www.bioconductor.org/help/mailing-list/ If I were you I'd search the mailing list first to see if someone else has asked a similar question. If not make a post. The developer of edgeR and other R bioconductor package ...
written 5.2 years ago by Jason20
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Comment: C: How do I obtain uniquely mappable reads from bowtie on galaxy?
... Ah, I totally didn't realize Galaxy had its own biostars forum. I guess I will submit the same question over there instead. Thanks for the heads up.   ...
written 5.2 years ago by Jason20
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How do I obtain uniquely mappable reads from bowtie on galaxy?
... Hello, I'm using bowtie on Galaxy to map my RNA-seq reads to the sacCer2 yeast ref genome. I was wondering which option or flag is responsible for making sure I have an output of uniquely mappable reads?  My workflow is the following: 1. Start with SOLiD output in the form of .csfasta reads and . ...
galaxy bowtie written 5.2 years ago by Jason20

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Popular Question 2.5 years ago, created a question with more than 1,000 views. For How do I obtain uniquely mappable reads from bowtie on galaxy?

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