User: biocyberman

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biocyberman700
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700
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Denmark
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5 days, 16 hours ago
Joined:
5 years, 6 months ago
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Posts by biocyberman

<prev • 114 results • page 1 of 12 • next >
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Comment: C: How to merge multiple tab-delimitated files
... If you guys have done some discussion before closing the question, I have nothing to say much about it. I will stop debating, but want to let you guys know my point of view: 'pure' (read impure) programming questions are often found here. tags of programming languages (i.e. Perl, Python, R, etc) ar ...
written 6 days ago by biocyberman700
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Comment: C: How to merge multiple tab-delimitated files
... IMO, it is not pure. He is trying to get help from other members who can share knowledge of how to deal with this data and use case. It's called networking and in bioinformatic context. I don't know who closed this question, or how it got closed. Anyway, there are tons of questions like this one on ...
written 16 days ago by biocyberman700
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Comment: C: biomaRt rnorvegicus_gene_ensembl dataset is not valid!
... I was using bioconductor version 3.5. I did not notice version of biomaRt. ...
written 5 weeks ago by biocyberman700
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Comment: C: biomaRt rnorvegicus_gene_ensembl dataset is not valid!
... I will wait a few days to confirm. Not feel like to provide an uncertain answer with 'seems' :) ...
written 5 weeks ago by biocyberman700
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Comment: A: Building STAR genome index continually killed
... Not quite answer the STAR's problem. But here is my approach for the same need: Although quite a bulky tool, I would rely on bcbio-nextgen to manage my aligner indexes and reference genome sequences: wget https://raw.github.com/bcbio/bcbio-nextgen/master/scripts/bcbio_nextgen_install.py py ...
written 5 weeks ago by biocyberman700
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biomaRt rnorvegicus_gene_ensembl dataset is not valid!
... Accessing to rat dataset is unstable during last few days. Sometimes it works, sometimes I get error like the following (R code): library(biomaRt) human = useEnsembl("ENSEMBL_MART_ENSEMBL", dataset = "hsapiens_gene_ensembl") # works fine rat = useEnsembl("ENSEMBL_MART_ENSEMBL", dataset ...
biomart written 5 weeks ago by biocyberman700 • updated 5 weeks ago by Mike Smith820
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Comment: C: extract isoform sequences of splicing variants?
... This would do for known isoforms in UCSC. I was thinking about something that can parse the isoform name (e.g. r.4357_4358ins4358-2785_4358-2719) and generate the sequence on the fly. ...
written 9 weeks ago by biocyberman700
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extract isoform sequences of splicing variants?
... Say I have this splicing variant (isoform): r.4357_4358ins4358-2785_4358-2719 And I have gene name BRCA1, and if necessary, reference transcript: https://www.ncbi.nlm.nih.gov/nuccore/NM_007294.3 What is the convenient way to get mRNA sequence of the isoform? **Update:** Would like to mention th ...
splicing rna-seq written 9 weeks ago by biocyberman700
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Convert COSMIC ID to dbSNP id?
... I downloaded data from COSMIC database, and now want to do batch conversion of the COSMIC ID to dbSNP id. For example, Cosmid variant: COSM425261 . What is the RS number of this SNP? I tried with biomart but did not work: http://www.ensembl.org/biomart/martview/def67ebf751f91c637ecbb873b20d4d1 ...
cosmic snp written 5 months ago by biocyberman700 • updated 5 months ago by Denise - Open Targets4.6k
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Job: Bioinformatician in Aalborg University Hospital, Denmark
... **Aalborg University Hospital Section of Molecular Diagnostics** We are looking for a motivated bioinformatician to strengthen and expand bioinformatic work force in response to increasing needs of a molecular diagnostic group utilizing big data. **Application deadline: 19th of April 2017** ** ...
denmark job bioinformatician written 17 months ago by biocyberman700

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Popular Question 9 weeks ago, created a question with more than 1,000 views. For Whole genome coordinates of promoters/gene regulatory elements
Popular Question 9 weeks ago, created a question with more than 1,000 views. For Tophat failed at 'Mapping left_kept_reads to transcriptome'
Good Answer 5 months ago, created an answer that was upvoted at least 5 times. For A: Venn diagram with 11 sets
Popular Question 5 months ago, created a question with more than 1,000 views. For Whole genome coordinates of promoters/gene regulatory elements
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Venn diagram with 11 sets
Appreciated 16 months ago, created a post with more than 5 votes. For A: Venn diagram with 11 sets
Popular Question 16 months ago, created a question with more than 1,000 views. For Tophat failed at 'Mapping left_kept_reads to transcriptome'
Popular Question 16 months ago, created a question with more than 1,000 views. For Why a de novo assembler is not a transcript assembler?
Popular Question 16 months ago, created a question with more than 1,000 views. For macs2 bdgdiff calculation without genomic background control?
Popular Question 16 months ago, created a question with more than 1,000 views. For Cookbook To Check Effects Of Nonsynonymous Snv To Mrna And Protein?
Popular Question 16 months ago, created a question with more than 1,000 views. For Programatically fetch all GI numbers for nucleotide sequences of a species from NCBI?
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Popular Question 20 months ago, created a question with more than 1,000 views. For Update Biopython'S Seqrecords?
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Scholar 2.3 years ago, created an answer that has been accepted. For A: Venn diagram with 11 sets
Teacher 2.3 years ago, created an answer with at least 3 up-votes. For A: Venn diagram with 11 sets
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Scholar 2.4 years ago, created an answer that has been accepted. For A: Venn diagram with 11 sets
Scholar 2.6 years ago, created an answer that has been accepted. For A: Venn diagram with 11 sets
Teacher 2.7 years ago, created an answer with at least 3 up-votes. For A: Tool for reducing contigs!!!!!!
Scholar 2.8 years ago, created an answer that has been accepted. For A: Venn diagram with 11 sets
Teacher 2.8 years ago, created an answer with at least 3 up-votes. For A: Tool for reducing contigs!!!!!!
Popular Question 3.0 years ago, created a question with more than 1,000 views. For Update Biopython'S Seqrecords?

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