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User: endrebak

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endrebak • 570
Reputation:
570
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5 days ago
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2 years ago
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https://www.ntnu.edu/employees/endrebak

https://github.com/endrebak

 

Posts by endrebak

<prev • 82 results • page 1 of 9 • next >
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Setting/finding the log odds detection threshold in custom homer PWMs
... I want to convert the JASPAR pwms to homer format: http://jaspar.genereg.net/downloads/ It seems like the JASPAR files in the transfac format are pretty close: AC MA0004.1 XX ID Arnt XX DE MA0004.1 Arnt ; From JASPAR 2018 PO A C G T 01 4.0 16.0 0.0 0.0 02 19.0 0.0 ...
homer jaspar motif written 28 days ago by endrebak • 570
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Comment: C: Dataset request: RNA-seq experiment that uses both single and paired end data wi
... Do you understand why they say "GSM461176–GSM461181" when GSM461182 etc are also seemingly from the same experiment? E.g. https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM461182 ...
written 9 weeks ago by endrebak • 570
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Comment: C: Dataset request: RNA-seq experiment that uses both single and paired end data wi
... Upvoted. Will accept when I get it downloaded :) Thanks :) Other suggestions also welcome :) ...
written 9 weeks ago by endrebak • 570
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Dataset request: RNA-seq experiment that uses both single and paired end data with multiple experimental conditions
... I want to find an RNA-seq experiment that uses both single and paired end data with multiple experimental conditions. It should be available in the public domain. Do any of you know such a dataset? If not, how can I search online databases to find such a dataset? Thanks, Endre ...
rna-seq sequencing written 9 weeks ago by endrebak • 570 • updated 9 weeks ago by Carlo Yague • 3.9k
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Comment: C: Snakemake vs. Nextflow: strengths and weaknesses
... Snakemake allows for conditional creation of the DAG and conditional execution of different code based on the input. ...
written 12 weeks ago by endrebak • 570
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Comment: C: Snakemake vs. Nextflow: strengths and weaknesses
... Snakemake has singularity support with the singularity directive. I haven't used nextflow, but I would be amazed if it is as flexible as Snakemake ...
written 12 weeks ago by endrebak • 570
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Comment: C: Convert VCF dosage file into dosage only file
... Missing an \n at the end :): bcftools query -f "%CHROM\t%POS[\t%DS]\n" minimac3.dose.vcf.gz ...
written 6 months ago by endrebak • 570
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Is bcf just a bgzipped vcf?
... 99% sure, but could not find the answer on google. Creating this q for other bcf newbs. ...
vcf bcf written 7 months ago by endrebak • 570
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Comment: C: How do I get a list of all species with a fasta genome in UCSC?
... Thanks, I actually wanted the abbrevs like hg38 and so on but this is good too. ...
written 9 months ago by endrebak • 570
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How do I get a list of all species with a fasta genome in UCSC?
... I want to get a list of all genomes in UCSC like mm10, hg38 etc. Is there a simple way to do that? ...
ucsc written 9 months ago by endrebak • 570 • updated 9 months ago by Matt Shirley ♦ 8.3k

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Popular Question 6 months ago, created a question with more than 1,000 views. For Script to compute the effective genome size: epic-effective
Popular Question 11 months ago, created a question with more than 1,000 views. For epic: new ChIP-Seq caller based on the SICER algorithm
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Scholar 20 months ago, created an answer that has been accepted. For A: Given a link that displays genome browser data, how do I download a pdf using a
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Appreciated 2.1 years ago, created a post with more than 5 votes. For epic: new ChIP-Seq caller based on the SICER algorithm
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