User: bisansamara

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bisansamara10
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Posts by bisansamara

<prev • 21 results • page 1 of 3 • next >
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Comment: C: Get variant position knowing the gene name, base change, and NM#
... This is super easy! Thanks. ...
written 8 months ago by bisansamara10
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Get variant position knowing the gene name, base change, and NM#
... I have a list of > 45 variants. I need to get the exact position of those variants (i.e. chr#:start-end) knowing the gene name affected, base change, and refseqID (NM#) for each variant. Below are few lines as an example of my data: Gene----------BaseChange----------refseqID MAN1B1------c.1897G ...
gene genome coordinates variant written 8 months ago by bisansamara10 • updated 8 months ago by Tao270
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Comment: C: Combining multiple files into a single text file in R
... Doesn't work, because multiple columns from matlab file could be joined together in the combined text file. It's not like each single column become a single row. ...
written 8 months ago by bisansamara10
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Comment: C: Combining multiple files into a single text file in R
... It's about the formatting needed before analysis. ...
written 8 months ago by bisansamara10
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Comment: C: Combining multiple files into a single text file in R
... Still doesn't work. Columns in matlab files become rows in text file. ...
written 8 months ago by bisansamara10
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(Closed) Combining multiple files into a single text file in R
... I have several matlab files which I need to read in R, and combine them into a single text file for further analysis. Each matlab file has 3 columns, and a different number of rows. Each column represents a numeric parameter to describe a single cell, and each row in an observation at a different ti ...
R datascience matlab code written 8 months ago by bisansamara10
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Invalid alternative alleles in ANNOVAR
... I have a text file with genetic variants, and I need to annotate them using ANNOVAR. I first have to convert the input file into ANNOVAR accepted format (vcf4). So when I run the following command: perl convert2annovar.pl test.txt -format vcf4 -allsample -withfreq > test.vcf4 I get this erro ...
annovar error allel annotation written 8 months ago by bisansamara10 • updated 8 months ago by Kevin Blighe37k
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Comment: C: Understanding the Notation of Genomic Variation Data
... The data is from those two papers: **(1)** Science. 2012 Dec 21;338(6114):1619-22. DOI 10.1126/science Supplementary table 11 **(2)** Nature. 2012 Apr 4;485(7397):246-50. DOI 10.1038/nature10989 Supplementary table 3. Your help is much appreciated! ...
written 9 months ago by bisansamara10
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Understanding the Notation of Genomic Variation Data
... I need help to understand following data: ref alt * 1D, -G * 2D, -CT * complex, +GG&-C * complex, -G & K at 242795103 * -CTTC/* So the full data has the chr# and positions of SNVs, in addition to the ref/alt nucleot ...
variants annovar nucleotides mutations annotation written 9 months ago by bisansamara10
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Comment: C: Identify the nearest common SNP to a given rare variant
... This seems like a good tool. But it's taking forever to convert the dbSNP file (downloaded from NCBI) from csv to bed....**any suggestions?** Note that I'm using Cygwin on Windows to run the commands. ...
written 11 months ago by bisansamara10

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