User: biocyberman

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biocyberman760
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Denmark
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Posts by biocyberman

<prev • 116 results • page 1 of 12 • next >
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Comment: C: How can I get only the rows when for the converge points : - +
... @Lila M: Make sure to check out the updated answer. I forgot to reset `pr` and `ps` (previous row, and previous sign) after printing. The updated version works correctly now. ...
written 4 months ago by biocyberman760
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Answer: A: How can I get only the rows when for the converge points : - +
... Haven't got an R solution yet, but these kind of manipulation I usually do with gawk/awk. Suppose your data file is in test.tsv. This is how you do it: gawk 'BEGIN{pr=""; ps=""}(ps == "-" && $4 == "+" ) {print pr; print; pr =""; ps =""; next}{ pr = $0; ps=$4}' test.tsv chr1 1 ...
written 4 months ago by biocyberman760
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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 5 months ago by biocyberman760
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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 5 months ago by biocyberman760
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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 6 months ago by biocyberman760
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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 6 months ago by biocyberman760
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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 6 months ago by biocyberman760
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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 6 months ago by biocyberman760 • updated 6 months ago by Mike Smith1.0k
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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 7 months ago by biocyberman760
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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 7 months ago by biocyberman760

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Scholar 4 months ago, created an answer that has been accepted. For A: Venn diagram with 11 sets
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Popular Question 7 months ago, created a question with more than 1,000 views. For Whole genome coordinates of promoters/gene regulatory elements
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Popular Question 11 months ago, created a question with more than 1,000 views. For Whole genome coordinates of promoters/gene regulatory elements
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Popular Question 22 months ago, created a question with more than 1,000 views. For Tophat failed at 'Mapping left_kept_reads to transcriptome'
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