User: alolex

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alolex890
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United States
Last seen:
2 years, 1 month ago
Joined:
3 years, 4 months ago
Email:
a*****@vcu.edu

I am a Bioinformatics Specialist with an educational background in Computer Science and extensive experience with analyzing microarray and HTS data.  I am also very familiar with accessing and analyzing public and private data from The Cancer Genome Atlas (TCGA).  I love to program in R and bash--bash mostly because it can weave together programs written in any language to create seamless automated workflows.  

Posts by alolex

<prev • 102 results • page 1 of 11 • next >
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Comment: C: Extract Sub-Set Of Regions From Vcf File
... Check to ensure your scaffold names match in the BED and VCF files. For example, if your BED file has "chr1" but your VCF file just has "1" for chromosome 1 it will return an empty file. ...
written 2.2 years ago by alolex890
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Comment: C: How To Convert Vcf File To Plink Ped Format?
... I am still new to using PLINK and variant calling in general, so someone with more experience may correct me if needed. For my purposes I generally have a VCF file that I need to convert to PLINK for certain things. When I do this I manually create the .fam file for all my samples. I'm not sure o ...
written 2.6 years ago by alolex890
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Comment: C: How do you define inter-disciplinary communication, how important are these skil
... Istvan, Thank you for your comment that my original post was oddly phrased--I agree.  I've tried to tackle it from a different direction.  If I don't get it right the first time I always try to re-think and re-phrase.   ...
written 3.0 years ago by alolex890
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Forum: How do you define inter-disciplinary communication, how important are these skills in your job and how frequently do you use them?
... Bioinformatics is an inter-disciplinary discipline that requires knowledge of biology, computer science, statistics, mathematics, medicine and more.  To me, inter-disciplinary communication does not just mean you can talk to a computational scientist or biological scientist, but it also means that y ...
forum written 3.0 years ago by alolex890 • updated 3.0 years ago by Dan Gaston7.1k
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Comment: C: how i can put bowtie2 with tophat2 in the path?
... Fereshteh, If you add the paths of bowtie2 and tophat2 to your $PATH then bowtie should be able to find tophat.  If you are on a Unix/Linux platform you can do this by: export PATH="$PATH:/path/to/bowtie2:/different/path/to/tophat2"; ...
written 3.1 years ago by alolex890
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Comment: C: Are there any workshops which are tailored to non-beginners/intermediate bioinfo
... Yes! I have been looking for this too.  Are any of these workshops for more advanced bioinformatics posted online anywhere?  Most of what I find is for beginners. ...
written 3.2 years ago by alolex890
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Answer: A: Cancer cell line WGS
... Have you checked ENCODE?  Search for "whole-genome" here: https://www.encodeproject.org/experiments It looks like they have fastq files for GM12878 and H1-hESC, but you may already have those from cgHub.   ...
written 3.2 years ago by alolex890
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Answer: A: Needed appropriate journal to submit my paper
... I assume you are referencing papers with somewhat similar topics.  You can look at where they were published to see if any would be appropriate for your paper.  Also, if you are working in a lab, or with an advisor, then they should be the ones paying for the publication, not you personally. ...
written 3.2 years ago by alolex890
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Answer: A: Draw multiple heatmaps
... You cannot do that with heatmap.2() due to the way it lays out the graph.  Try the aheatmap() function from the NMF package.  You should be able to use the layout() command with these heatmaps. ...
written 3.2 years ago by alolex890
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Answer: A: How to filter genes by gene size
... The information you seek just requires a little leg work.  Go to the UCSC table browser (see link from seidel), select the group as "Genes and Gene Predictions" and the appropriate track for your project.  Then select your region to be "genome", and select the output format to be "selected fields fr ...
written 3.2 years ago by alolex890

Latest awards to alolex

Centurion 2.6 years ago, created 100 posts.
Commentator 2.7 years ago, created a comment with at least 3 up-votes. For C: Extract reads within given region, and their mates
Good Answer 2.9 years ago, created an answer that was upvoted at least 5 times. For A: Why is DESeq a better method for finding highly upregulated and downregulated ge
Scholar 3.1 years ago, created an answer that has been accepted. For A: scripting problem to change string match of one file to another
Teacher 3.2 years ago, created an answer with at least 3 up-votes. For A: scripting problem to change string match of one file to another
Teacher 3.2 years ago, created an answer with at least 3 up-votes. For A: scripting problem to change string match of one file to another
Teacher 3.2 years ago, created an answer with at least 3 up-votes. For A: scripting problem to change string match of one file to another
Commentator 3.2 years ago, created a comment with at least 3 up-votes. For C: Extract reads within given region, and their mates
Rising Star 3.3 years ago, created 50 posts within first three months of joining.
Scholar 3.3 years ago, created an answer that has been accepted. For A: scripting problem to change string match of one file to another
Scholar 3.3 years ago, created an answer that has been accepted. For A: scripting problem to change string match of one file to another
Supporter 3.3 years ago, voted at least 25 times.
Scholar 3.3 years ago, created an answer that has been accepted. For A: scripting problem to change string match of one file to another
Scholar 3.4 years ago, created an answer that has been accepted. For A: How to work with Level 3 data (RPKM values) from TCGA database
Scholar 3.4 years ago, created an answer that has been accepted. For A: How to work with Level 3 data (RPKM values) from TCGA database
Teacher 3.4 years ago, created an answer with at least 3 up-votes. For A: How to work with Level 3 data (RPKM values) from TCGA database
Autobiographer 3.4 years ago, has more than 80 characters in the information field of the user's profile.
Scholar 3.4 years ago, created an answer that has been accepted. For A: How to work with Level 3 data (RPKM values) from TCGA database
Teacher 3.4 years ago, created an answer with at least 3 up-votes. For A: How to work with Level 3 data (RPKM values) from TCGA database

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