User: endrebak

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endrebak570
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570
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5 days ago
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2 years ago
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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 endrebak570
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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 endrebak570
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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 endrebak570
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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 endrebak570 • updated 9 weeks ago by Carlo Yague3.9k
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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 endrebak570
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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 endrebak570
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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 endrebak570
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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 endrebak570
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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 endrebak570
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8 follow
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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 endrebak570 • updated 9 months ago by Matt Shirley8.3k

Latest awards to endrebak

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
Teacher 16 months ago, created an answer with at least 3 up-votes. For A: How To Convert Gencode Gtf Into Bed Format ?
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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
Student 20 months ago, asked a question with at least 3 up-votes. For Fast datastructure to get counts of overlapping reads per nucleotide (!) in Python?
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Appreciated 2.0 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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Appreciated 2.1 years ago, created a post with more than 5 votes. For epic: new ChIP-Seq caller based on the SICER algorithm
Student 2.1 years ago, asked a question with at least 3 up-votes. For epic: new ChIP-Seq caller based on the SICER algorithm
Commentator 2.1 years ago, created a comment with at least 3 up-votes. For C: SICER raw data

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