User: Roman Valls Guimerà

Reputation:
520
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Trusted
Location:
Melbourne
Website:
https://blogs.nopcode....
Twitter:
@braincode
Last seen:
1 month ago
Joined:
9 years, 4 months ago
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b*********@nopcode.org

Posts by Roman Valls Guimerà

<prev • 58 results • page 1 of 6 • next >
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Comment: C: Tool for random access to indexed BAM files in S3?
... See: https://www.biostars.org/p/385688/#385818 ...
written 4 weeks ago by Roman Valls Guimerà520
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Comment: C: Using samtools to view an indexed file in a private S3 bucket
... Also, make sure you keep the AWSAccessKeyId, signature, etc... parameters after the '?' on your `samtools view` command, otherwise the (presigned) URL will not be accessible. ...
written 4 weeks ago by Roman Valls Guimerà520
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Job: RSE and Bioinformatics positions for the University of Melbourne for Cancer Research
... Please follow this link and apply!: https://twitter.com/fiamh/status/1128462516177129472 ...
bioinformatics rse job written 7 weeks ago by Roman Valls Guimerà520
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News: Integrative Genomic Viewer (IGV) works with Amazon S3
... Still on its way to get accepted upstream, but it works well for us so far: https://blog.umccr.org/2019/02/16/igv-amazon/ Hope it helps! ...
news amazon igv written 5 months ago by Roman Valls Guimerà520
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Answer: A: Where Can I Download Some Bam Files?
... For a quick-gratification one-liner (instead of multi-step and multi-MB approaches), one could just use that command (after installing samtools): samtools view -h ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase1/data/HG00154/alignment/HG00154.mapped.ILLUMINA.bwa.GBR.low_coverage.20101123.bam 17 ...
written 8 months ago by Roman Valls Guimerà520
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Comment: C: Snakemake vs. Nextflow: strengths and weaknesses
... The table is outdated by now, Snakemake does support Kubernetes AFAICT: https://snakemake.readthedocs.io/en/stable/executable.html#executing-a-snakemake-workflow-via-kubernetes ...
written 14 months ago by Roman Valls Guimerà520
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Answer: A: Is There An Easy Way Of Getting Gene Symbols From Genomic Coordinates?
... In today's (2018) `cruzdb` it seems to require a bit more work than that since one has to iterate/fetchall through the sql query (also give the intervals with integers instead of `str`): In [9]: from cruzdb import Genome ...: hg18 = Genome('hg18') ...: hg18.bin_query('refGene', 'chr1' ...
written 15 months ago by Roman Valls Guimerà520
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Is there a standalone VCF file anonymizer tool?
... While tracking down a bug by yet another VCF parsing/filtering script, I realized that trimming a VCF is quite tedious and prone to shaving the actual bug while doing so while preparing the test case. Does anybody know of a VCF randomizer/anonymizer/fuzzer that would allow me to share (cancer) sens ...
vcf written 2.2 years ago by Roman Valls Guimerà520
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Answer: A: TCGA tumor/normal RNA-seq somatic mutation calling
... Perhaps you can give a try to [this one][1]? [1]: https://bcbio-nextgen.readthedocs.org/en/latest/contents/pipelines.html#cancer-variant-calling ...
written 3.4 years ago by Roman Valls Guimerà520 • updated 10 months ago by RamRS22k
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Answer: A: Retrieve expression data from Allen Brain Atlas API
... Sorry for announcing it here, but perhaps you'll have more luck/answers in the sister [Neuro community of BioStars][1]. Disclaimer: shameless plug since I enacted it :P [1]: https://neurostars.org ...
written 3.4 years ago by Roman Valls Guimerà520 • updated 10 months ago by RamRS22k

Latest awards to Roman Valls Guimerà

Good Answer 2.2 years ago, created an answer that was upvoted at least 5 times. For A: Distributed Computing In Bioinformatics
Teacher 3.2 years ago, created an answer with at least 3 up-votes. For A: Alternatives To Galaxy For Wrapping Command Line Tools In A Graphical User Inter
Epic Question 3.8 years ago, created a question with more than 10,000 views. For Generating .Vcf.Idx Files From Cmdline
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Good Question 4.7 years ago, asked a question that was upvoted at least 5 times. For Faster Illumina Analysis Pipeline Via Streaming
Appreciated 4.7 years ago, created a post with more than 5 votes. For C: Cloud Computing Real Implication On Bioinformatics
Popular Question 4.7 years ago, created a question with more than 1,000 views. For Generating .Vcf.Idx Files From Cmdline
Great Question 4.9 years ago, created a question with more than 5,000 views. For Generating .Vcf.Idx Files From Cmdline
Supporter 5.5 years ago, voted at least 25 times.
Teacher 6.3 years ago, created an answer with at least 3 up-votes. For A: Distributed Computing In Bioinformatics
Student 7.6 years ago, asked a question with at least 3 up-votes. For Faster Illumina Analysis Pipeline Via Streaming
Appreciated 7.6 years ago, created a post with more than 5 votes. For Faster Illumina Analysis Pipeline Via Streaming
Teacher 7.7 years ago, created an answer with at least 3 up-votes. For A: Alternatives To Galaxy For Wrapping Command Line Tools In A Graphical User Inter
Popular Question 7.7 years ago, created a question with more than 1,000 views. For Generating .Vcf.Idx Files From Cmdline
Teacher 8.1 years ago, created an answer with at least 3 up-votes. For A: What Is The Best Pipeline For Human Whole Exome Sequencing?
Popular Question 8.3 years ago, created a question with more than 1,000 views. For Sample Identifier Standard For Lims Systems ?
Good Question 8.3 years ago, asked a question that was upvoted at least 5 times. For Sample Identifier Standard For Lims Systems ?
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Appreciated 8.7 years ago, created a post with more than 5 votes. For C: Cloud Computing Real Implication On Bioinformatics
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